Mammalian proteinases; oxidoreductases; related reagents

ABSTRACT

Nucleic acids encoding various proteases, from a mammal, reagents related thereto, including specific antibodies, and purified proteins are described. Methods of using said reagents and related diagnostic kits are also provided.

FIELD OF THE INVENTION

[0001] The present invention contemplates compositions related toproteins from animals, e.g., mammals, which function as proteinases; oroxidoreductases. In particular, it provides nucleic acids which encode,antibodies to, and proteins which exhibit biological functions, e.g.,capacity to degrade proteinaceous substrates or serve asoxidoreductases.

BACKGROUND OF THE INVENTION

[0002] The proteases are a very broad group of enzymes which carry outan enzymatic function of hydrolysing a peptide bond. Within the group,there is a wide range of substrate specificities for the amino acidsadjacent the cleavage sites. Proteases are typically categorized on thebasis of their catalytic mecahnisms, e.g., based upon studies of theiractive sites, or by the effects of pH. Four main categories of proteasesare serine proteinases, sulfhydryl proteases, acid proteases, andmetalloproteases. They may also be classified according to theircleavage sites, e.g., endoproteases, amino peptidases, or carboxypeptidases.

[0003] Proteases have traditionally held a large share of the industrialenzyme market. Proteases are used in many industrial processes,including in detergents and cleaning products, e.g., to degrade proteinmaterials such as blood and stains, in leather production, e.g., toremove hair, in baking, e.g., to break down glutens, in flavorings,e.g., soy sauce, in meat tenderizing, e.g., to break down collagen, ingelatin or food supplement production, in the textile industry, in wastetreatment, and in the photographic industry. See, e.g., Gusek (1991)Inform 1:14-18; Zamost, et al. (1996) J. Industrial Microbiol. 8:71-82;James and Simpson (1996) CRC Critical Reviews in Food Science andNutrition 36:437-463; Teichgraeber, et al. (1993) Trends in Food Scienceand Technology 4:145-149; Tjwan, et al. (1993) J. Dairy Research60:269-286; Haard (1992) J. Aquatic Food Product Technology 1:17-35; vanDijk (1995) Laundry and Cleaning News 21:32-33; Nolte, et al. (1996) J.Textile Institute 87:212-226; Chikkodi, et al. (1995) Textile Res. J.65:564-569; and Shih (1993) Poultry Science 72:1617-1620.

[0004] Oxidoreductases are involved in oxidation and reductionreactions, and have important functions, e.g., in oxidativephosphorylation. These enzymes are important in electron transport andgeneral aerobic metabolism, and in many cases are associated with themitochondrial membranes. In various circumstances, it may be useful tomodulate oxidoreductase reactions to slow down or increase energymetabolism, e.g., in a cell or organ.

[0005] While there are many uses for proteases, there is always the needfor a more active protease under various specific conditions. Similarly,regulation of oxidoreduction may be important. Alternatively, thedistribution of these gene products may be useful as markers forspecific cell or tissue types. There is a need for new proteinases oroxidoreductase enzymes of differing properties, specificities, andactivities.

SUMMARY OF THE INVENTION

[0006] The present invention provides a binding compound comprising anantibody binding site which specifically binds to primate BS10.55protein; or primate YTF03 protein; a nucleic acid comprising sequenceencoding at least 12 amino acids of primate BS10.55 protein; or primateYTF03 protein; a substantially pure protein which is specificallyrecognized by the above antibody binding site; a substantially pureprimate BS10.55, or primate YTF03 protein or peptide thereof; and afusion protein comprising a 30 amino acid sequence portion of primateBS10.55, or primate YTF03 protein sequence.

[0007] In certain binding compound embodiments, the antibody bindingsite is specifically immunoreactive with a protein selected frompolypeptides of SEQ ID NO: 2 and 4; is raised against a purified orrecombinantly produced primate BS10.55, or primate YTF03 protein; isimmunoselected on a substantially purified or recombinantly producedprimate BS10.55, or primate YTF03 protein; is in a monoclonal antibody,Fab, or F(ab)₂; is detectably labeled; is attached to a solid substrate;is from a rabbit or mouse; binds with a Kd of at least about 300 μM; isfused to another protein segment; is in a chimeric antibody; or iscouped to another chemical moiety.

[0008] The invention also provides a method of making anantigen-antibody complex, comprising a step of contacting a primatebiological sample to a specific binding antibody described. In preferredembodiments, the method further includes steps to purify the antigen orantibody.

[0009] Alternative embodiments provide an antibody binding site whereinthe binding site is detected in a biological sample by a methodcomprising the steps of contacting a binding agent having an affinityfor BS10.55 or YTF03 protein with the biological sample; incubating thebinding agent with the biological sample to form a binding agent:BS10.55or binding agent:YTF03 protein complex; and detecting the complex. Incertain embodiments, the biological sample is human, and the bindingagent is an antibody.

[0010] The invention also provides kits containing a compositiondescribed above and instructional material for the use of thecomposition; or segregation of the composition into a container.Typically, the kit is used to make a qualitative or quantitativeanalysis.

[0011] The invention also embraces a cell comprising an antibodydescribed above; a cell transfected with a nucleic acid described above;or a cell comprising a fusion protein described above.

[0012] In nucleic acid embodiments, the nucleic acid may encode apolypeptide which specifically binds an antibody generated against animmunogen selected from the group consisting of the mature polypeptidesof SEQ ID NO: 2 and 4. Alternatively, the nucleic acid may encode atleast 12 amino acids of SEQ ID NO: 2 or SEQ ID NO: 4; comprise sequenceof at least about 39 nucleotides selected from protein coding portionsof SEQ ID NO: 1 or 3; hybridize to SEQ ID NO: 1 or 3 under stringentwash conditions of at least 45° C. and less than about 150 mM salt;comprise sequence made by a synthetic method; be an expression vector;be detectably labeled; be attached to a solid substrate; be from human;bind with a Kd of at least about 300 μM; be fused to another nucleicacid segment; be coupled to another chemical moiety; be operablyassociated with promoter, ribosome binding site, or poly-A additionsite; be a PCR product; be transformed into a cell, including abacterial cell; be in a sterile composition; be capable of selectivelyhybridizing to a nucleic acid encoding a BS10.55, or YTF03 protein;comprise a natural sequence; comprise a mature protein coding segment ofSEQ ID NO: 1 or 3; encode proteolytically active portion of BS10.55;encode an oxidoreductive active portion of YTF03; be detected in abiological sample by a method comprising: contacting a biological samplewith a nucleic acid probe capable of selectively hybridizing to saidnucleic acid, incubating the nucleic acid probe with the biologicalsample to form a hybrid of the nucleic acid probe with complementarynucleic acid sequences present in the biological sample; and determiningthe extent of hybridization of the nucleic acid probe to thecomplementary nucleic acid sequences, including the method where thenucleic acid probe is capable of hybridizing to a nucleic acid encodinga protein selected from the group consisting of the mature polypeptidesof SEQ ID NO 2 and 4.

[0013] In protein or polypeptide embodiments, the proteins may bind witha Kd of at least about 300 μM to an antibody generated against animmunogen of the polypeptides of SEQ ID NO: 2 or 4; be immunoselected onan antibody which selectively binds a polypeptide of SEQ ID NO: 2 or 4;comprise sequence of at least 12 contiguous residues of SEQ ID NO: 2 or4; exhibit a post-translational modification pattern distinct fromnatural BS10.55, or YTF03; be 3-fold or fewer substituted from naturalsequence; be recombinantly produced; be denatured; have sequence of fulllength natural polypeptide; be detectably labeled; be attached to asolid substrate; be from human; be in a sterile composition; be fused toanother protein segment; be coupled to another chemical moiety; compriseat least a fragment of at least 32 amino acid residues from a humanBS10.55, or human YTF03 protein; comprise mature polypeptide sequenceselected from the group consisting of SEQ ID NO 2 and 4; be a solubleprotein; be a naturally occurring protein; be a proteolytically activeportion of BS10.55; or be an oxidoreductive active portion of YTF03.

[0014] The invention also provides an isolated protein whichspecifically binds to an antibody generated against an immunogenselected from the group consisting of the full length polypeptides ofSEQ ID NO: 2 or 4. Preferably such protein binds to the antibody with aKd of at least about 300 μM; is immunoselected on an antibody whichselectively binds a polypeptide of SEQ ID NO: 2 or 4; comprises sequenceof at least 12 contiguous residues of SEQ ID NO: 2 or 4; exhibits apost-translational modification pattern distinct from natural BS10.55,.or YTF03; is 3-fold or fewer substituted from natural sequence; isrecombinantly produced; is denatured; has sequence of full lengthnatural polypeptide; is detectably labeled; is attached to a solidsubstrate; is from human; is in a sterile composition; is fused toanother protein segment; is coupled to another chemical moiety;comprises at least a fragment of at least 32 amino acid residues from ahuman BS10.55, or human YTF03 protein; comprises mature polypeptidesequence selected from the group consisting of SEQ ID NO 2 and 4; is asoluble protein; comprises a proteolytic activity of BS10.55; orcomprises an oxidoreductive activity of YTF03.

[0015] In certain other embodiments, the invention embraces a fusionprotein described above, which comprises sequence from an enzymaticallyactive portion of SEQ ID NO: 2 or 4. Preferably such protein binds witha Kd of at least about 300 μM to an antibody generated against animmunogen having sequence of a polypeptide of SEQ ID NO. 2 or 4; isimmunoselected on an antibody which selectively binds a polypeptide ofSEQ ID NO: 2 or 4; comprises sequence of at least 12 contiguous residuesof SEQ ID NO: 2 or 4; is recombinantly produced; is denatured; hassequence of full length natural polypeptide; is detectably labeled; isattached to a solid substrate; comprises sequence from human; is in asterile composition; is fused to another protein segment; is coupled toanother chemical moiety; comprises at least a fragment of at least 32amino acid residues from a human BS10.55, or human YTF03 protein;comprises mature polypeptide sequence selected from the group consistingof SEQ ID NO 2 and 4; is a soluble protein; comprises a proteolyticactivity of BS10.55; or comprises an oxidoreductive activity of YTF03.

[0016] The invention also provides a substantially pure proteindescribed above which comprises a proteolytic activity of BS10.55; or anoxidoreductive activity of YTF03.

[0017] A method of modulating physiology or development of a cellcomprising contacting said cell with said compositions is provided.

[0018] Likewise, the invention provides a binding compound comprising anantibody binding site which specifically binds to primate APD08; anucleic acid comprising sequence encoding at least 12 amino acids ofprimate APD08; a substantially pure protein which is specificallyrecognized by the antibody binding site; a substantially pure primateAPD08 protein or peptide thereof, and; a fusion protein comprising a 30amino acid sequence portion of primate APD08 protein sequence.

DETAILED DESCRIPTION

[0019] Outline

[0020] I. General

[0021] II. Definitions

[0022] III. Nucleic Acids

[0023] IV. Making BS10.55 or YTF03 Protein

[0024] V. Antibodies; binding compounds

[0025] a. antibody production

[0026] b. immunoassays

[0027] VI. Purified BS10.55 and YTF03 Protein

[0028] VII. Physical Variants

[0029] VIII. Binding Agent: BS10.55 or YTF03 Protein Complexes

[0030] IX. Functional Variants

[0031] X. Uses

[0032] XI. Kits

[0033] XII. Substrate Identification

[0034] I. General

[0035] The present invention provides DNA sequences encoding mammalianproteins which exhibit structural properties or motifs characteristic ofa protease; or an oxidoreductase. The proteins described herein aredesignated BS10.55 and YTF03. See Tables 1 and 2.

[0036] The descriptions below are directed, for exemplary purposes, toprimate embodiments, e.g., human, but are likewise applicable to relatedembodiments from other, e.g., natural, sources. These sources should,where appropriate, include various vertebrates, typically warm bloodedanimals, e.g., birds and mammals, particularly domestic animals, andprimates. TABLE 1 Human BS10.55 nucleotide and predicted amino acidsequence. SEQ ID NO: 1 and 2. The initiation methionine indicates onepossible start codon, though a second, perhaps more probable, initiationcodon encodes the methionine at position 14. A hydrophobic regionfollows the latter, which may be a signal sequence running, e.g., toabout Ala30; and a mature processed form may begin in the range of27-33, probably Ile31. CGCCCGGGCA GGTGAGAAAT TGGAGAAGAT AAAACTGGACACTGGGGAGA CCACAACTTC 60 ATG CTG CGT GGG ATC TCC CAG CTA CCT GCA GTG GCCACC ATG TCT TGG 108 Met Leu Arg Gly Ile Ser Gln Leu Pro Ala Val Ala ThrMet Ser Trp   1               5                  10                  15GTC CTG CTG CCT GTA CTT TGG CTC ATT GTT CAA ACT CAA GCA ATA GCC 156 ValLeu Leu Pro Val Leu Trp Leu Ile Val Gln Thr Gln Ala Ile Ala             20                  25                  30 ATA AAG CAA ACACCT GAA TTA ACG CTC CAT GAA ATA GTT TGT CCT AAA 204 Ile Lys Gln Thr ProGlu Leu Thr Leu His Glu Ile Val Cys Pro Lys         35                  40                  45 AAA CTT CAC ATT TTACAC AAA AGA GAG ATC AAG AAC AAC CAG ACA GAA 252 Lys Leu His Ile Leu HisLys Arg Glu Ile Lys Asn Asn Gln Thr Glu     50                  55                  60 AAG CAT GGC AAA GAG GAAAGG TAT GAA CCT GAA GTT CAA TAT CAG ATG 300 Lys His Gly Lys Glu Glu ArgTyr Glu Pro Glu Val Gln Tyr Gln Met 65                  70                  75                  80 ATC TTAAAT GGA GAA GAA ATC ATT CTC TCC CTA CAA AAA ACC AAG CAC 348 Ile Leu AsnGly Glu Glu Ile Ile Leu Ser Leu Gln Lys Thr Lys His                 85                  90                  95 CTC CTG GGGCCA GAC TAC ACT GAA ACA TTG TAC TCA CCC AGA GGA GAG 396 Leu Leu Gly ProAsp Tyr Thr Glu Thr Leu Tyr Ser Pro Arg Gly Glu            100                 105                 110 GAA ATT ACC ACGAAA CCT GAG AAC ATG GAA CAC TGT TAC TAT AAA GGA 444 Glu Ile Thr Thr LysPro Glu Asn Met Glu His Cys Tyr Tyr Lys Gly        115                 120                 125 AAC ATC CTA AAT GAAAAG AAT TCT GTT GCC AGC ATC AGT ACT TGT GAC 492 Asn Ile Leu Asn Glu LysAsn Ser Val Ala Ser Ile Ser Thr Cys Asp    130                 135                 140 GGG TTG AGA GGA TAC TTCACA CAT CAT CAC CAA AGA TAC CAG ATA AAA 540 Gly Leu Arg Gly Tyr Phe ThrHis His His Gln Arg Tyr Gln Ile Lys145                 150                 155                 160 CCT CTGAAA AGC ACA GAC GAG AAA GAA CAT GCC GTC TTT ACA TCT AAC 588 Pro Leu LysSer Thr Asp Glu Lys Glu His Ala Val Phe Thr Ser Asn                165                 170                 175 CAG GAG GAACAA GAC CCA GCT AAC CAC ACA TGT GGT GTG AAG AGC ACT 636 Gln Glu Glu GlnAsp Pro Ala Asn His Thr Cys Gly Val Lys Ser Thr            180                 185                 190 GAC GGG AAA CAAGGC CCA ATT CGA ATC TCT AGA TCA CTC AAA AGC CCA 684 Asp Gly Lys Gln GlyPro Ile Arg Ile Ser Arg Ser Leu Lys Ser Pro        195                 200                 205 GAG AAA GAA GAC TTTCTT CGG GCA CAG AAA TAC ATT GAT CTC TAT TTG 732 Glu Lys Glu Asp Phe LeuArg Ala Gln Lys Tyr Ile Asp Leu Tyr Leu    210                 215                 220 GTG CTG GAT AAT GCC TTTTAT AAG AAC TAT AAT GAG AAT CTA ACT CTG 780 Val Leu Asp Asn Ala Phe TyrLys Asn Tyr Asn Glu Asn Leu Thr Leu225                 230                 235                 240 ATA AGAAGC TTT GTG TTT GAT GTG ATG AAC CTA CTC AAT GTG ATA TAT 828 Ile Arg SerPhe Val Phe Asp Val Met Asn Leu Leu Asn Val Ile Tyr                245                 250                 255 AAC ACC ATAGAT GTT CAA GTG GCC TTG GTA GGT ATG GAA ATC TGG TCT 876 Asn Thr Ile AspVal Gln Val Ala Leu Val Gly Met Glu Ile Trp Ser            260                 265                 270 GAT GGG GAT AAGATA AAG GTG GTG CCC AGC GCA AGC ACC ACG TTT GAC 924 Asp Gly Asp Lys IleLys Val Val Pro Ser Ala Ser Thr Thr Phe Asp        275                 280                 285 AAC TTC CTG AGA TGGCAC AGT TCT AAC CCG GGG AAA AAG ATC CAC GAC 972 Asn Phe Leu Arg Trp HisSer Ser Asn Pro Gly Lys Lys Ile His Asp    290                 295                 300 CAT GCT CAG CTT CTC AGCGGG ATT AGC TTC AAC AAT CGA CGT GTG GGA 1020 His Ala Gln Leu Leu Ser GlyIle Ser Phe Asn Asn Arg Arg Val Gly305                 310                 315                 320 CTG GCAGCT TCA AAT TCC TTG TGT TCC CCA TCT TCG GTT GCT GTT ATT 1068 Leu Ala AlaSer Asn Ser Leu Cys Ser Pro Ser Ser Val Ala Val Ile                325                 330                 335 GAG GCT AAAAAA AAG AAT AAT GTG GCT CTT GTA GGA GTG ATG TCA CAT 1116 Glu Ala Lys LysLys Asn Asn Val Ala Leu Val Gly Val Met Ser His            340                 345                 350 GAG CTG GGC CATGTC CTT GGT ATG CCT GAT GTT CCA TTC AAC ACC AAG 1164 Glu Leu Gly His ValLeu Gly Met Pro Asp Val Pro Phe Asn Thr Lys        355                 360                 365 TGT CCC TCT GGC AGTTGT GTG ATG AAT CAG TAT CTG AGT TCA AAA TTC 1212 Cys Pro Ser Gly Ser CysVal Met Asn Gln Tyr Leu Ser Ser Lys Phe    370                 375                 380 CCA AAG GAT TTC AGT ACATCT TGC CGT GCA CAT TTT GAA AGA TAC CTT 1260 Pro Lys Asp Phe Ser Thr SerCys Arg Ala His Phe Glu Arg Tyr Leu385                 390                 395                 400 TTA TCTCAG AAA CCA AAG TGC CTG CTG CAA GCA CCT ATT CCT ACA AAT 1308 Leu Ser GlnLys Pro Lys Cys Leu Leu Gln Ala Pro Ile Pro Thr Asn                405                 410                 415 ATA ATG ACAACA CCA GTG TGT GGG AAC CAC CTT CTA GAA GTG GGA GAA 1356 Ile Met Thr ThrPro Val Cys Gly Asn His Leu Leu Glu Val Gly Glu            420                 425                 430 GAC TGT GAT TGTGGC TCT CCT AAG GAG TGT ACC AGT CTC TGC TGT GAA 1404 Asp Cys Asp Cys GlySer Pro Lys Glu Cys Thr Ser Leu Cys Cys Glu        435                 440                 445 GCC CTA ACG TGT AAACTG AAG CCT GGA ACT GAT TGC GGA GGA GAT GCT 1452 Ala Leu Thr Cys Lys LeuLys Pro Gly Thr Asp Cys Gly Gly Asp Ala    450                 455                 460 CCA AAC CAT ACC ACA GAGTGA ATCCAAAGTC TGCTTCACTG AGATGCTACC 1503 Pro Asn His Thr Thr Glu  *465                 470 TTGCCAGGAC AAGAACCAAG AACTCTAACT GTCCCAGGAATCTTGTGAAT TTTCACCCAT 1563 AATGGTCTTT CACTTGTCAT TCTACTTTCT ATATTGTTATCAGTCCAGGA AACAGGTAAA 1623 CAGATGTAAT TAGAGACATT GGCTCTTTGT TTAGGCCTAATCTTTCTTTT TACTTTTTTT 1683 TTTCTTTTTT CTTTTTTTTT AAAGATCATG AATTTGTGACTTAGTTCTGC CCTTTGGAGA 1743 ACAAAAGAAA GCAGTCTTCC ATCAAATCAC CTTAAAATGCACGGCTAAAC TATTCAGAGT 1803 TAACACTCCA GAATTGTTAA ATTACAAGTA CTATGCTTTAATGCTTCTTT CATCTTACTA 1863 GTATGGCCTA TAAAAAAAAT AATACCACTT GATGGGTGAAGGCTTTGGCA ATAGAAAGAA 1923 GAATAGAATT CAGGTTTTAT GTTATTCCTC TGTGTTCACTTCGCCTTGCT CTTGAAAGTG 1983 CAGTATTTTT CTACATCATG TCGAGAATGA TTCAATGTAAATATTTTTCA TTTTATCATG 2043 TATATCCTAT ACACACATCT CCTTCATCAT CATATATGAAGTTTATTTTG AGAAGTCTAC 2103 ATTGCTTACA TTTTAATTGA GCCAGCAAAG AAGGCTTAATGATTTATTGA ACCATAATGT 2163 CAATAAAAAC ACAACTTTTG AGGCAAAAAA AAAAAAAAAAAAAAAAAAAA AAAAAAAAAA 2223 AAAAAAAAAA AAAAAAAAAG AAAAAAAAAA AAAAAAAAAAAAAGACCTGC CCGGGCG 2280

[0037] TABLE 2 Human YTF03 monoamine oxiase-like gene nucleic acid andpredicted amino acid sequence. SEQ ID NO: 3 and 4. The predicted signalsequence would run, e.g., to about gln22; and a mature processed formmay begin in the range of 18-25, probably asp23. Putative transmembranesegments run from about val62 to leu78; and ala272 to ala289. Amitochondrial localization motif is near gln22. AGTGGAGAGG ACCGCGCTGTCCTGCTGTCA CCAAGAGCTG GAGACACCAT CTCCCACCGA 60 GAGTC ATG GCC CCA TTG GCCCTG CAC CTC CTC GTC CTC GTC CCC ATC 107       Met Ala Pro Leu Ala LeuHis Leu Leu Val Leu Val Pro Ile        1               5                  10 CTC CTC AGC CTG GTG GCCTCC CAG GAC TGG AAG GCT GAA CGC AGC CAA 155 Leu Leu Ser Leu Val Ala SerGln Asp Trp Lys Ala Glu Arg Ser Gln 15                  20                  25                  30 GAC CCCTTC GAG AAA TGC ATG CAG GAT CCT GAC TAT GAG CAG CTG CTC 203 Asp Pro PheGlu Lys Cys Met Gln Asp Pro Asp Tyr Glu Gln Leu Leu                 35                  40                  45 AAG GTG GTGACC TGG GGG CTC AAT CGG ACC CTG AAG CCC CAG AGG GTG 251 Lys Val Val ThrTrp Gly Leu Asn Arg Thr Leu Lys Pro Gln Arg Val             50                  55                  60 ATT GTG GTT GGCGCT GGT GTG GCC GGG CTG GTG GCC GCC AAG GTG CTC 299 Ile Val Val Gly AlaGly Val Ala Gly Leu Val Ala Ala Lys Val Leu         65                  70                  75 AGC GAT GCT GGA CACAAG GTC ACC ATC CTG GAG GCA GAT AAC AGG ATC 347 Ser Asp Ala Gly His LysVal Thr Ile Leu Glu Ala Asp Asn Arg Ile     80                  85                  90 GGG GGC CGC ATC TTC ACCTAC CGG GAC CAG AAC ACG GGC TGG ATT GGG 395 Gly Gly Arg Ile Phe Thr TyrArg Asp Gln Asn Thr Gly Trp Ile Gly 95                 100                 105                 110 GAG CTGGGA GCC ATG CGC ATG CCC AGC TCT CAC AGG ATC CTC CAC AAG 443 Glu Leu GlyAla Met Arg Met Pro Ser Ser His Arg Ile Leu His Lys                115                 120                 125 CTC TGC CAGGGC CTG GGG CTC AAC CTG ACC AAG TTC ACC CAG TAC GAC 491 Leu Cys Gln GlyLeu Gly Leu Asn Leu Thr Lys Phe Thr Gln Tyr Asp            130                 135                 140 AAG AAC ACG TGGACG GAG GTG CAC GAA GTG AAG CTG CGC AAC TAT GTG 539 Lys Asn Thr Trp ThrGlu Val His Glu Val Lys Leu Arg Asn Tyr Val        145                 150                 155 GTG GAG AAG GTG CCCGAG AAG CTG GGC TAC GCC TTG CGT CCC CAG GAA 587 Val Glu Lys Val Pro GluLys Leu Gly Tyr Ala Leu Arg Pro Gln Glu    160                 165                 170 AAG GGC CAC TCG CCC GAAGAC ATC TAC CAG ATG GCT CTC AAC CAG GCC 635 Lys Gly His Ser Pro Glu AspIle Tyr Gln Met Ala Leu Asn Gln Ala175                 180                 185                 190 CTC AAAGAC CTC AAG GCA CTG GGC TGC AGA AAG GCG ATG AAG AAG TTT 683 Leu Lys AspLeu Lys Ala Leu Gly Cys Arg Lys Ala Met Lys Lys Phe                195                 200                 205 GAA AGG CACACG CTC TTG GAA TAT CTT CTC GGG GAG GGG AAC CTG AGC 731 Glu Arg His ThrLeu Leu Glu Tyr Leu Leu Gly Glu Gly Asn Leu Ser            210                 215                 220 CGG CCG GCC GTGCAG CTT CTG GGA GAC GTG ATG TCC GAG GAT GGC TTC 779 Arg Pro Ala Val GlnLeu Leu Gly Asp Val Met Ser Glu Asp Gly Phe        225                 230                 235 TTC TAT CTC AGC TTCGCC GAG GCC CTC CGG GCC CAC AGC TGC CTC AGC 827 Phe Tyr Leu Ser Phe AlaGlu Ala Leu Arg Ala His Ser Cys Leu Ser    240                 245                 250 GAC AGA CTC CAG TAC AGCCGC ATC GTG GGT GGC TGG GAC CTG CTG CCG 875 Asp Arg Leu Gln Tyr Ser ArgIle Val Gly Gly Trp Asp Leu Leu Pro255                 260                 265                 270 CGC GCGCTG CTG AGC TCG CTG TCC GGG CTT GTG CTG TTG AAC GCG CCC 923 Arg Ala LeuLeu Ser Ser Leu Ser Gly Leu Val Leu Leu Asn Ala Pro                275                 280                 285 GTG GTG GCGATG ACC CAG GGA CCG CAC GAT GTG CAC GTG CAG ATC GAG 971 Val Val Ala MetThr Gln Gly Pro His Asp Val His Val Gln Ile Glu            290                 295                 300 ACC TCT CCC CCGGCG CGG AAT CTG AAG GTG CTG AAG GCC GAC GTG GTG 1019 Thr Ser Pro Pro AlaArg Asn Leu Lys Val Leu Lys Ala Asp Val Val        305                 310                 315 CTG CTG ACG GCG AGCGGA CCG GCG GTG AAG CGC ATC ACC TTC TCG CCG 1067 Leu Leu Thr Ala Ser GlyPro Ala Val Lys Arg Ile Thr Phe Ser Pro    320                 325                 330 CCG CTG CCC CGC CAC ATGCAG GAG GCG CTG CGG AGG CTG CAC TAC GTG 1115 Pro Leu Pro Arg His Met GlnGlu Ala Leu Arg Arg Leu His Tyr Val335                 340                 345                 350 CCG GCCACC AAG GTG TTC CTA AGC TTC CGC AGG CCC TTC TGG CGC GAG 1163 Pro Ala ThrLys Val Phe Leu Ser Phe Arg Arg Pro Phe Trp Arg Glu                355                 360                 365 GAG CAC ATTGAA GGC GGC CAC TCA AAC ACC GAT CGC CCG TCG CGC ATG 1211 Glu His Ile GluGly Gly His Ser Asn Thr Asp Arg Pro Ser Arg Met            370                 375                 380 ATT TTC TAC CCGCCG CCG CGC GAG GGC GCG CTG CTG CTG GCC TCG TAC 1259 Ile Phe Tyr Pro ProPro Arg Glu Gly Ala Leu Leu Leu Ala Ser Tyr        385                 390                 395 ACG TGG TCG GAC GCGGCG GCA GCG TTC GCC GGC TTG AGC CGG GAA GAG 1307 Thr Trp Ser Asp Ala AlaAla Ala Phe Ala Gly Leu Ser Arg Glu Glu    400                 405                 410 GCG TTG CGC TTG GCG CTCGAC GAC GTG GCG GCA TTG CAC GGG CCT GTC 1355 Ala Leu Arg Leu Ala Leu AspAsp Val Ala Ala Leu His Gly Pro Val415                 420                 425                 430 GTG CGCCAG CTC TGG GAC GGC ACC GGC GTC GTC AAG CGT TGG GCG GAG 1403 Val Arg GlnLeu Trp Asp Gly Thr Gly Val Val Lys Arg Trp Ala Glu                435                 440                 445 GAC CAG CACAGC CAG GGT GGC TTT GTG GTA CAG CCG CCG GCG CTC TGG 1451 Asp Gln His SerGln Gly Gly Phe Val Val Gln Pro Pro Ala Leu Trp            450                 455                 460 CAA ACC GAA AAGGAT GAC TGG ACG GTC CCT TAT GGC CGC ATC TAC TTT 1499 Gln Thr Glu Lys AspAsp Trp Thr Val Pro Tyr Gly Arg Ile Tyr Phe        465                 470                 475 GCC GGC GAG CAC ACCGCC TAC CCG CAC GGC TGG GTG GAG ACG GCG GTC 1547 Ala Gly Glu His Thr AlaTyr Pro His Gly Trp Val Glu Thr Ala Val    480                 485                 490 AAG TCG GCG CTG CGC GCCGCC ATC AAG ATC AAC AGC CGG AAG GGG CCT 1595 Lys Ser Ala Leu Arg Ala AlaIle Lys Ile Asn Ser Arg Lys Gly Pro495                 500                 505                 510 GCA TCGGAC ACG GCC AGC CCC GAG GGG CAC GCA TCT GAC ATG GAG GGG 1643 Ala Ser AspThr Ala Ser Pro Glu Gly His Ala Ser Asp Met Glu Gly                515                 520                 525 CAG GGG CATGTG CAT GGG GTG GCC AGC AGC CCC TCG CAT GAC CTG GCA 1691 Gln Gly His ValHis Gly Val Ala Ser Ser Pro Ser His Asp Leu Ala            530                 535                 540 AAG GAA GAA GGCAGC CAC CCT CCA GTC CAA GGC CAG TTA TCT CTC CAA 1739 Lys Glu Glu Gly SerHis Pro Pro Val Gln Gly Gln Leu Ser Leu Gln        545                 550                 555 AAC ACG ACC CAC ACGAGG ACC TCG CAT TAA AGTATTTTCG G 1780 Asn Thr Thr His Thr Arg Thr SerHis  *     560                 565

[0038] The proteins of this invention are defined in part by theirsequences, and by their physicochemical and biological properties. Thebiological properties of the human proteases described herein, e.g.,human BS10.55, and oxidoreductases, e.g., human YTF03, are defined bytheir amino acid sequences, and mature sizes. They also should sharecertain biological enzymatic properties of their respective proteins.

[0039] The human protease YTF03 translation product exhibits structuralmotifs of a member of the metalloproteinase family of proteases, morespecifically to a family of disintegrin-metalloproteinases. Theseproteins, in the latent form, typically possess a prodomain form whichmasks the catalytic site, which chelates a zinc ion. See Vallee and Auld(1990) Biochemistry 29:5647-5659. The processed mature protein istypically a potent cell-matrix degrading enzyme. See, e.g.,Birkedal-Hansen (1990) Proc. Nat'l Acad, Sci. USA 87:5578-5582. Distinctfrom the family of strictly matrix-metalloproteinases (see, e.g.,Birkedal-Hansen, et al. (1993) Crit. Rev. Oral. Biol, Med. 4:197-250),the disintegrin-metalloproteinases comprise, besides the zinc-chelatingdomain, a 90 amino acid disintegrin cysteine rich domain. See, e.g.,Hite, et al. (1992) Biochemistry 31:6203-6211. This domain bindsintegrin cell adhesion molecules and can disrupt cell-matrixinteractions. Gould, et al. (1990) Proc. Soc. Exp. Biol. Med.195:168-171. It is postulated that the disintegrin moiety supports thecatalytic domain in recognising and specifically cleaving matrixsubstrates. A large number of disintegrins are found in snake venoms,which inhibit platelet aggregation by competing with fibrinogen forbinding to the platelet's glycoprotein IIb-IIa complex. The mammaliandisintegrin-metalloproteinases include fertilin α (Blobel, et al. (1992)Nature 356:248-252), meltrin (Yagami-Hiromasa, et al. (1995) Nature377:652-656), MS2 (Yoshida, et al. (1990) Int. Immunol. 2:585-591), EAP1(Perry, et al. (1992) Biochem J. 286:671-675), and ADAMTS (Kuno, et al.(1997) J. Biol. Chem. 272:556-562). Fertilin α and meltrin are likely tobe membrane proteins and are thought involved in cell-cell fusion via afusion peptide similar to virus envelope proteins. EAP1 and MS2 alsocontain a transmembrane spanning region, and ADAMTS comprisesthrombospondin motifs. Interestingly, MS2 seems specifically expressedby mouse macrophages but its function is unclear.

[0040] BS10.55 contains the zinc binding peptide consensus at residues352-359 of SEQ ID NO: 2 (His-Glu-Met/Leu-Gly-His-X-X-Gly) and thedisintegrin homology lies between SEQ ID NO: 2 residues 430-460 shortlybefore the end of the open reading frame. The peptide motif at residues187-189 (Cys-Gly-Val) is characteristic of the prodomain (Hite, et al.(1992) Biochemistry 31:6203-6211). BS10.55 exhibits a hydrophobic regionfollowing the second methinone (at 14) at the 5′ end of the cDNAsequence, likely to be a signal sequence. This, and the lack of aputative transmembrane region, suggest that this noveldisintegrin-metalloproteinases is secreted. Natural substrates for theproteinase may be identified using standard methods. Substrate sequencespecificity may be determined, and search for such sequences indatabases may identify specific candidates for physiological substrates.

[0041] The YTF03 gene was initially found by analysis of clones isolatedfrom germinal center dendritic cells. This cDNA is distantly related toa family of enzymes which include monamine oxidases (MOAs). Theseproteins are typically mitochondrial outer membrane proteins found in atleast two forms and are tissue restricted to, e.g., certain neurons andastrocytes. They generally function to oxidatively deaminate, e.g.,vasoactive and neuroactive amines, and are often targets foramphetamines. The YTF03 product does not have the key residues whichcovalently bind the classical MOA's FAD cofactor, and so it may notexhibit monamine oxidase activity itself. The protein is most closelyrelated to a hypothesized protein from a cyanobacteria, but onlyslightly more so than to other MOAs. The predicted protein has aconvincing leader sequence, though it may have characteristics whichsuggest association with intracellular membranous compartments likeother MOAs. It is evident that the overall structure of the body of theORF is very strongly conserved. Despite the relatively low homology withits relatives, there is little tolerance for addition/deletion changes(+/−1 residue) in certain regions. This suggests an intricate structuralmix of alpha helices and beta sheets. PCR analysis suggests that YTF03mRNA is expressed mainly in Dendritic Cells (DC) and monocytes, and to alesser extent in some T cells.

[0042] A comparison search versus the GenPep database gave closest matchto the sequence ACCESSION 1001515 cyanobacterium Synechocystis sp.hypothetical protein. Viewing the structure, there is fairly believableconservation of helix/sheet paterns, though the cyano ORF has no leaderand is a little shortened at the C-terminus.

[0043] One of skill will readily recognize that some sequence variationsmay be tolerated, e.g., conservative substitutions or positions remotefrom the critical helical structures and remote from the identified orconsensus critial active site regions, without altering significantlythe biological activity of each respective molecule.

[0044] BS10.55 or YTF03 proteins are present in specific cell types,e.g., dendritic cells, and the interaction of the protease with asubstrate will be important for mediating various aspects of cellularphysiology or development. The cellular types which express messagesencoding APG02 and YTF03 suggest that signals important in celldifferentiation and development are mediated by them. See, e.g., Gilbert(1991) Developmental Biology (3d ed.) Sinauer Associates, Sunderland,Mass.; Browder, et al. (1991) Developmental Biology (3d ed.) Saunders,Philadelphia, Pa.; Russo, et al. (1992) Development: The MolecularGenetic Approach Springer-Verlag, New York, N.Y.; and Wilkins (1993)Genetic Analysis of Animal Development (2d ed.) Wiley-Liss, New York,N.Y. In particular, the proteases may be necessary for the conversion ofpro-proteins to proteins, e.g., cytokine or protein precursors to matureforms, or for proper immunological function, e.g., antigen processingand presentation.

[0045] II. Definitions

[0046] The term “binding composition” refers to molecules that bind withspecificity to BS10.55 or YTF03, respectively, e.g., in anantibody-antigen interaction. However, other compounds, e.g., complexassociated proteins, may also specifically associate with BS10.55 orYTF03 to the exclusion of other molecules. Typically, the associationwill be in a natural physiologically relevant protein-proteininteraction, either covalent or non-covalent, and may include members ofa multiprotein complex, including carrier compounds or dimerizationpartners. The molecule may be a polymer, or chemical reagent. Afunctional analog may be a protease with structural modifications, ormay be a wholly unrelated molecule, e.g., which has a molecular shapewhich interacts with the appropriate substrate cleavage determinants.

[0047] The term “binding agent:BS10.55 or YTF03 protein complex”, asused herein, refers to a complex of a binding agent and a BS10.55 orYTF03 protein that is formed by specific binding of the binding agent tothe BS10.55 or YTF03 protein. Specific binding of the binding agentmeans that the binding agent has a specific binding site that recognizesa site on the BS10.55 or YTF03 protein, typically in the nativeconformation, but possibly in a denatured conformation, e.g., a Westernblot. For example, antibodies raised to a BS10.55 or YTF03 protein andrecognizing an epitope on the BS10.55 or YTF03 protein are capable offorming a binding agent:BS10.55 or binding agent:YTF03 protein complexby specific binding. Typically, the formation of a binding agent:BS10.55or YTF03 protein complex allows the measurement of BS10.55 or YTF03protein in a biological sample, e.g., a mixture with other proteins andbiologics. The term “antibody:BS10.55 or antibody:YTF03 protein complex”refers to an embodiment in which the binding agent is an antibody. Theantibody may be monoclonal, polyclonal, or a binding fragment of anantibody, e.g, an Fab, F(ab)₂, or Fv fragment. The antibody willpreferably be a polyclonal antibody for cross-reactivity determinations.

[0048] “Homologous” nucleic acid sequences, when compared, exhibitsignificant similarity or identity. The standards for homology innucleic acids are either measures for homology generally used in the artby sequence comparison and/or phylogenetic relationship, or based uponhybridization conditions. Hybridization conditions are described ingreater detail below.

[0049] An “isolated” nucleic acid is a nucleic acid, e.g., an RNA, DNA,or a mixed polymer, which is substantially separated from other biologiccomponents which naturally accompany a native sequence, e.g., proteinsand flanking genomic sequences from the originating species. The termembraces a nucleic acid sequence which has been removed from itsnaturally occurring environment, and includes recombinant or cloned DNAisolates and chemically synthesized analogs, or analogs biologicallysynthesized by heterologous systems. A substantially pure moleculeincludes isolated forms of the molecule. An isolated nucleic acid willusually contain homogeneous nucleic acid molecules, but will, in someembodiments, contain nucleic acids with minor sequence heterogeneity.This heterogeneity is typically found at the polymer ends or portionsnot critical to a desired biological function or activity.

[0050] As used herein, the term “BS10.55” or “YTF03” protein shallencompass, when used in a protein context, a protein having amino acidsequences, particularly from the protein motif portions, shown in SEQ IDNO: 2 or 4, respectively. In many contexts, a significant fragment ofsuch a protein will be functionally equivalent. The invention alsoembraces a polypeptide which exhibits similar structure to human BS10.55or YTF03 protein, e.g., which interacts with BS10.55 or YTF03 specificbinding components. These binding components, e.g., antibodies,typically bind to BS10.55 or YTF03 protein with high affinity, e.g., atleast about 100 nM, usually better than about 30 nM, preferably betterthan about 10 nM, and more preferably at better than about 3 nM.

[0051] The term “polypeptide” or “protein” as used herein includes asignificant fragment or segment of protease motif portion of BS10.55 orYTF03 protein, and encompasses a stretch of amino acid residues of atleast about 8 amino acids, generally at least about 10 amino acids, moregenerally at least about 12 amino acids, often at least about 14 aminoacids, more often at least about 16 amino acids, typically at leastabout 18 amino acids, more typically at least about 20 amino acids,usually at least about 22 amino acids, more usually at least about 24amino acids, preferably at least about 26 amino acids, more preferablyat least about 28 amino acids, and, in particularly preferredembodiments, at least about 30 or more amino acids, e.g., 35, 40, 45,50, 60, 70, 80, 100, etc.

[0052] A “recombinant” nucleic acid is defined either by its method ofproduction or its structure. In reference to its method of production,e.g., a product made by a process, the process is use of recombinantnucleic acid techniques, e.g., involving human intervention in thenucleotide sequence, typically selection or production. Alternatively,it can be a nucleic acid made by generating a sequence comprising fusionof two fragments which are not naturally contiguous to each other, butis meant to exclude products of nature, e.g., naturally occurringmutants. Thus, for example, products made by transforming cells with anynon-naturally occurring vector is encompassed, as are nucleic acidscomprising sequence derived using any synthetic oligonucleotide process.Such is often done to replace a codon with a redundant codon encodingthe same or a conservative amino acid, while typically introducing orremoving a sequence recognition site. Alternatively, it is performed tojoin together nucleic acid segments of desired functions to generate asingle genetic entity comprising a desired combination of functions notfound in the commonly available natural forms. Restriction enzymerecognition sites are often the target of such artificial manipulations,but other site specific targets, e.g., promoters, DNA replication sites,regulation sequences, control sequences, or other useful features may beincorporated by design. A similar concept is intended for a recombinant,e.g., fusion, polypeptide. Specifically included are synthetic nucleicacids which, by genetic code redundancy, encode polypeptides similar tofragments of these antigens, and fusions of sequences from variousdifferent species variants.

[0053] “Solubility” is reflected by sedimentation measured in Svedbergunits, which are a measure of the sedimentation velocity of a moleculeunder particular conditions. The determination of the sedimentationvelocity was classically performed in an analytical ultracentrifuge, butis typically now performed in a standard ultracentrifuge. See,Freifelder (1982) Physical Biochemistry (2d ed.) W. H. Freeman & Co.,San Francisco, Calif.; and Cantor and Schimmel (1980) BiophysicalChemistry parts 1-3, W. H. Freeman & Co., San Francisco, Calif. As acrude determination, a sample containing a putatively solublepolypeptide is spun in a standard full sized ultracentrifuge at about50K rpm for about 10 minutes, and soluble molecules will remain in thesupernatant. Asoluble particle or polypeptide will typically be lessthan about 30S, more typically less than about 15S, usually less thanabout 10S, more usually less than about 6S, and, in particularembodiments, preferably less than about 4S, and more preferably lessthan about 3S. Solubility of a polypeptide or fragment depends upon theenvironment and the polypeptide. Many parameters affect polypeptidesolubility, including temperature, electrolyte environment, size andmolecular characteristics of the polypeptide, and nature of the solvent.Typically, the temperature at which the polypeptide is used ranges fromabout 4° C. to about 65° C. Usually the temperature at use is greaterthan about 18° C. and more usually greater than about 22° C. Fordiagnostic purposes, the temperature will usually be about roomtemperature or warmer, but less than the denaturation temperature ofcomponents in the assay. For therapeutic purposes, the temperature willusually be body temperature, typically about 37° C. for humans, thoughunder certain situations the temperature may be raised or lowered insitu or in vitro.

[0054] The size and structure of the polypeptide should generally be ina substantially stable state, and usually not in a denatured state. Thepolypeptide may be associated with other polypeptides in a quaternarystructure, e.g., to confer solubility, or associated with lipids ordetergents in a manner which approximates natural lipid bilayerinteractions.

[0055] The solvent will usually be a biologically compatible buffer, ofa type used for preservation of biological activities, and will usuallyapproximate a physiological solvent. Usually the solvent will have aneutral pH, typically between about 5 and 10, and preferably about 7.5.On some occasions, a detergent will be added, typically a mildnon-denaturing one, e.g., CHS (cholesteryl hemisuccinate) or CHAPS(3-[3-cholamidopropyl)-dimethylammonio]-1-propane sulfonate), or a lowenough concentration as to avoid significant disruption of structural orphysiological properties of the protein.

[0056] “Substantially pure” in a protein context typically means thatthe protein is isolated from other contaminating proteins, nucleicacids, and other biologicals derived from the original source organism.Purity, or “isolation” may be assayed by standard methods, and willordinarily be at least about 50% pure, more ordinarily at least about60% pure, generally at least about 70% pure, more generally at leastabout 80% pure, often at least about 85% pure, more often at least about90% pure, preferably at least about 95% pure, more preferably at leastabout 98% pure, and in most preferred embodiments, at least 99% pure.Similar concepts apply, e.g., to antibodies or nucleic acids.

[0057] “Substantial similarity” in the nucleic acid sequence comparisoncontext means either that the segments, or their complementary strands,when compared, are identical when optimally aligned, with appropriatenucleotide insertions- or deletions, in at least about 50% of thenucleotides, generally at least about 56%, more generally at least about59%, ordinarily at least about 62%, more ordinarily at least about 65%,often at least about 68%, more often at least about 71%, typically atleast about 74%, more typically at least about 77%, usually at leastabout 80%, more usually at least about 85%, preferably at least about90%, more preferably at least about 95 to 98% or more, and in particularembodiments, as high at about 99% or more of the nucleotides.Alternatively, substantial similarity exists when the segments willhybridize under selective hybridization conditions, to a strand, or itscomplement, typically using a sequence derived from SEQ ID NO: 1 or 3.Typically, selective hybridization will occur when there is at leastabout 55% similarity over a stretch of at least about 30 nucleotides,preferably at least about 65% over a stretch of at least about 25nucleotides, more preferably at least about 75%, and most preferably atleast about 90% over about 20 nucleotides. See Kanehisa (1984) Nuc.Acids Res. 12:203-213. The length of similarity comparison, asdescribed, may be over longer stretches, and in certain embodiments willbe over a stretch of at least about 17 nucleotides, usually at leastabout 20 nucleotides, more usually at least about 24 nucleotides,typically at least about 28 nucleotides, more typically at least about40 nucleotides, preferably at least about 50 nucleotides, and morepreferably at least about 75 to 100 or more nucleotides, e.g., 150, 200,etc.

[0058] “Stringent conditions”, in referring to homology or substantialsimilarity in the hybridization context, will be stringent combinedconditions of salt, temperature, organic solvents, and other parameters,typically those controlled in hybridization reactions. The combinationof parameters is generally more important than the measure of any singleparameter. See, e.g., Wetmur and Davidson (1968) J. Mol. Biol.31:349-370. A nucleic acid probe which binds to a target nucleic acidunder stringent conditions is specific for said target nucleic acid.Such a probe is typically more than 11 nucleotides in length, and issufficiently identical or complementary to a target nucleic acid overthe region specified by the sequence of the probe to bind the targetunder stringent hybridization conditions.

[0059] BS10.55 or YTF03 proteins from other mammalian species can becloned and isolated by cross-species hybridization of closely relatedspecies. See, e.g., below. Similarity may be relatively low betweendistantly related species, and thus hybridization of relatively closelyrelated species is advisable. Alternatively, preparation of an antibodypreparation which exhibits less species specificity may be useful inexpression cloning approaches.

[0060] The phrase “specifically binds to an antibody” or “specificallyimmunoreactive with”, when referring to a protein or peptide, refers toa binding reaction which is determinative of the presence of the proteinin the presence of a heterogeneous population of proteins and otherbiological components. Thus, under designated immunoassay conditions,the specified antibodies bind to a particular protein and do notsignificantly bind other proteins present in the sample. Specificbinding to an antibody under such conditions may require an antibodythat is selected for its specificity for a particular protein. Forexample, antibodies raised to the human BS10.55 or YTF03 proteinimmunogen with the amino acid sequence depicted in SEQ ID NO: 2 or 4 canbe selected by immunoaffinity or similar methods to obtain antibodiesspecifically immunoreactive with BS10.55 or YTF03 proteins and not withother proteins.

[0061] III. Nucleic Acids

[0062] BS10.55 or YTF03 proteins are exemplary of larger classes ofstructurally and functionally related proteins. The BS10.55 proteinswill typically serve to cleave or process various proteins produced orprocessed by various cell types, e.g., for antigen presentation. Thepreferred embodiments, as disclosed, will be useful in standardprocedures to isolate genes from different individuals or other species,e.g., warm blooded animals, such as birds and mammals. Crosshybridization will allow isolation of related genes encoding proteinsfrom individuals, strains, or species. A number of different approachesare available to successfully isolate a suitable nucleic acid clonebased upon the information provided herein. Southern blot hybridizationstudies can qualitatively determine the presence of homologous genes inhuman, monkey, rat, dog, cow, and rabbit genomes under specifichybridization conditions.

[0063] Complementary sequences will also be used as probes or primers.Based upon identification of the likely amino terminus, other peptidesshould be particularly useful, e.g., coupled with anchored vector orpoly-A complementary PCR techniques or with complementary DNA of otherpeptides.

[0064] Techniques for nucleic acid manipulation of genes encodingBS10.55 or YTF03 proteins, such as subcloning nucleic acid sequencesencoding polypeptides into expression vectors, labelling probes, DNAhybridization, and the like are described generally in Sambrook, et al.(1989) Molecular Cloning: A Laboratory Manual (2nd ed.) Vol. 1-3, ColdSpring Harbor Laboratory, Cold Spring Harbor Press, NY, which isincorporated herein by reference. This manual is hereinafter referred toas “Sambrook, et al.”.

[0065] There are various methods of isolating DNA sequences encodingBS10.55 or YTF03 proteins. For example, DNA is isolated from a genomicor cDNA library using labeled oligonucleotide probes having sequencesidentical or complementary to the sequences disclosed herein.Full-length probes may be used, or oligonucleotide probes may begenerated by comparison of the sequences disclosed. Such probes can beused directly in hybridization assays to isolate DNA encoding BS10.55 orYTF03 proteins, or probes can be designed for use in amplificationtechniques such as PCR, for the isolation of DNA encoding BS10.55 orYTF03 proteins.

[0066] To prepare a cDNA library, mRNA is isolated from cells,preferably which express high levels of a BS10.55 or YTF03 protein cDNAis prepared from the mRNA and ligated, e.g., into a recombinant vector.The vector is transfected into a recombinant host for propagation,screening, and cloning. Methods for making and screening cDNA librariesare well known. See Gubler and Hoffman (1983) Gene 25:263-269 andSambrook, et al.

[0067] For a genomic library, the DNA can be extracted from tissue, andoften either mechanically sheared or enzymatically digested to yieldfragments of about 12-20 kb. The fragments are then separated bygradient centrifugation and cloned in bacteriophage lambda vectors.These vectors and phage are packaged in vitro, as described in Sambrook,et al. Recombinant phage are analyzed by plaque hybridization asdescribed in Benton and Davis (1977) Science 196:180-182. Colonyhybridization is carried out as generally described in, e.g., Grunstein,et al. (1975) Proc. Natl. Acad. Sci. USA. 72:3961 3965.

[0068] DNA encoding a BS10.55 or YTF03 protein can be identified ineither cDNA or genomic libraries by its ability to hybridize with thenucleic acid probes described herein, e.g., in colony or plaquehybridization assays. The corresponding DNA regions are isolated, e.g.,by standard methods familiar to those of skill in the art. See, e.g.,Sambrook, et al.

[0069] Various methods of amplifying target sequences, such as thepolymerase chain reaction, can also be used to prepare DNA encodingBS10.55 or YTF03 proteins. Polymerase chain reaction (PCR) technologymay be used to amplify such nucleic acid sequences directly from mRNA,from cDNA, and/or from genomic libraries or cDNA libraries. The isolatedsequences encoding BS10.55 or YTF03 proteins may also be used astemplates for PCR amplification.

[0070] Typically, in PCR techniques, oligonucleotide primerscomplementary to two flanking regions in the DNA region to be amplifiedare synthesized. The polymerase chain reaction is then carried out usingthe two primers. See Innis, et al. (eds.) (1990) PCR Protocols: A Guideto Methods and Applications Academic Press, San Diego, Calif. Primerscan be selected to amplify the entire regions encoding a full-lengthhuman BS10.55 or YTF03 protein or to amplify smaller DNA segments, asdesired. Once such regions are PCR-amplified, they can be sequenced andoligonucleotide probes can be prepared from sequence obtained usingstandard techniques. These probes can then be used to isolate DNA'sencoding BS10.55 or YTF03 proteins.

[0071] Oligonucleotides for use as probes are usually chemicallysynthesized according to the solid phase phosphoramidite triester methodfirst described by Beaucage and Carruthers (1983) Tetrahedron Lett.22(20):1859-1862, or using an automated synthesizer, as described inNeedham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168.Purification of oligonucleotides is performed e.g., by native acrylamidegel electrophoresis or by anion-exchange HPLC as described in Pearsonand Regnier (1983) J. Chrom. 255:137-149. The sequence of the syntheticoligonucleotide can be verified using, e.g., the chemical degradationmethod of Maxam, A. M. and Gilbert, W. in Grossman, L. and Moldave(eds.) (1980) Methods in Enzymology 65:499-560 Academic Press, New York.

[0072] An isolated nucleic acid encoding a human BS10.55 or YTF03protein was identified. The nucleotide sequence, corresponding openreading frames, and mature peptides are provided in Tables 1 or and SEQID NO: 1-4.

[0073] This invention provides isolated DNA or fragments to encode aBS10.55 or YTF03 protein or specific fragment thereof. In addition, thisinvention provides isolated or recombinant DNA which encodes a proteinor polypeptide, and which is capable of hybridizing under appropriateconditions, e.g., high stringency, with the DNA sequences describedherein. Said biologically active protein or polypeptide can be afunctional protease or oxidoreductase segment, or fragment, and have anamino acid sequence as disclosed in SEQ ID NO: 2 or 4. Preferredembodiments will be full length natural sequences, from isolates, orproteolytic fragments thereof. Further, this invention contemplates theuse of isolated or recombinant DNA, or fragments thereof, which encodeproteins which exhibit high measures of identity to a BS10.55 or YTF03protein, or which were isolated, e.g., using cDNA encoding a BS10.55protease or YTF03 oxidoreductase protein as a probe. The isolated DNAcan have the respective regulatory sequences in the 5′ and 3′ flanks,e.g., promoters, enhancers, poly-A addition signals, and others.

[0074] IV. Making Human BS10.55 or YTF03 Proteins

[0075] DNAs which encode a BS10.55 or YTF03 protein, or fragmentsthereof, can be obtained by chemical synthesis, screening cDNAlibraries, or by screening genomic libraries prepared from a widevariety of cell lines or tissue samples.

[0076] These DNAs can be expressed in a wide variety of host cells forthe synthesis of a full-length protein or fragments which can in turn,e.g., be used to generate polyclonal or monoclonal antibodies; forbinding studies; for construction and expression of modified molecules;and for structure/function studies. Each of BS10.55 or YTF03, or theirfragments, can be expressed in host cells that are transformed ortransfected with appropriate expression vectors. These molecules can besubstantially purified to be free of protein or cellular contaminants,other than those derived from the recombinant host, and therefore areparticularly useful in pharmaceutical compositions when combined with apharmaceutically acceptable carrier and/or diluent. The antigen, e.g.,BS10.55 or YTF03, or portions thereof, may be expressed as fusions withother proteins or possessing an epitope tag.

[0077] Expression vectors are typically self-replicating DNA or RNAconstructs containing the desired antigen gene or its fragments, usuallyoperably linked to appropriate genetic control elements that arerecognized in a suitable host cell. The specific type of controlelements necessary to effect expression will depend upon the eventualhost cell used. Generally, the genetic control elements can include aprokaryotic promoter system or a eukaryotic promoter expression controlsystem, and typically include a transcriptional promoter, an optionaloperator to control the onset of transcription, transcription enhancersto elevate the level of mRNA expression, a sequence that encodes asuitable ribosome binding site, and sequences that terminatetranscription and translation. Expression vectors also usually containan origin of replication that allows the vector to replicateindependently from the host cell.

[0078] The vectors of this invention contain DNAs which encode a BS10.55or YTF03 protein, or a significant fragment thereof, typically encoding,e.g., a biologically active polypeptide, or protein. The DNA can beunder the control of a viral promoter and can encode a selection marker.This invention further contemplates use of such expression vectors whichare capable of expressing eukaryotic cDNA coding for a BS10.55 or YTF03protein in a prokaryotic or eukaryotic host, where the vector iscompatible with the host and where the eukaryotic cDNA coding for theprotein is inserted into the vector such that growth of the hostcontaining the vector expresses the cDNA in question. Usually,expression vectors are designed for stable replication in their hostcells or for amplification to greatly increase the total number ofcopies of the desirable gene per cell. It is not always necessary torequire that an expression vector replicate in a host cell, e.g., it ispossible to effect transient expression of the protein or its fragmentsin various hosts using vectors that do not contain a replication originthat is recognized by the host cell. It is also possible to use vectorsthat cause integration of a BS10.55 or YTF03 protein gene or itsfragments into the host DNA by recombination, or to integrate a promoterwhich controls expression of an endogenous gene.

[0079] Vectors, as used herein, contemplate plasmids, viruses,bacteriophage, integratable DNA fragments, and other vehicles whichenable the integration of DNA fragments into the genome of the host.Expression vectors are specialized vectors which contain genetic controlelements that effect expression of operably linked genes. Plasmids arethe most commonly used form of vector, but many other forms of vectorswhich serve an equivalent function are suitable for use herein. See,e.g., Pouwels, et al. (1985 and Supplements) Cloning Vectors: ALaboratory Manual Elsevier, N.Y.; and Rodriquez, et al. (eds.) (1988)Vectors: A Survey of Molecular Cloning Vectors and Their UsesButtersworth, Boston, Mass.

[0080] Suitable host cells include prokaryotes, lower eukaryotes, andhigher eukaryotes. Prokaryotes include both gram negative and grampositive organisms, e.g., E. coli and B. subtilis. Lower eukaryotesinclude yeasts, e.g., S. cerevisiae and Pichia, and species of the genusDictyostelium. Higher eukaryotes include established tissue culture celllines from-animal cells, both of non-mammalian origin, e.g., insectcells, and birds, and of mammalian origin, e.g., human, primates, androdents.

[0081] Prokaryotic host-vector systems include a wide variety of vectorsfor many different species. As used herein, E. coli and its vectors willbe used generically to include equivalent vectors used in otherprokaryotes. A representative vector for amplifying DNA is pBR322 or itsderivatives. Vectors that can be used to express BS10.55 or YTF03proteins or fragments thereof include, but are not limited to, suchvectors as those containing the lac promoter (pUC-series); trp promoter(pBR322-trp); Ipp promoter (the pIN-series); lambda-pP or pR promoters(pOTS); or hybrid promoters such as ptac (pDR540). See Brosius, et al.(1988) “Expression Vectors Employing Lambda-, trp-, lac-, andIpp-derived Promoters”, in Rodriguez and Denhardt (eds.) Vectors: ASurvey of Molecular Cloning Vectors and Their Uses 10:205-236Buttersworth, Boston, Mass.

[0082] Lower eukaryotes, e.g., yeasts and Dictyostelium, may betransformed with BS10.55- or YTF03-protein sequence containing vectors.For purposes of this invention, the most common lower eukaryotic host isthe baker's yeast, Saccharomyces cerevisiae. It will be used genericallyto represent lower eukaryotes although a number of other strains andspecies will be essentially equivalent. Yeast vectors typically consistof a replication origin (unless of the integrating type), one or moreselection genes, a promoter, DNA encoding the desired protein or itsfragments, and sequences for translation termination, polyadenylation,and transcription termination. Suitable expression vectors for yeastinclude such constitutive promoters as 3-phosphoglycerate kinase andvarious other glycolytic enzyme gene promoters or such induciblepromoters as the alcohol dehydrogenase 2 promoter or metallothioninepromoter. Suitable vectors include derivatives of the following types:self-replicating low copy number (such as the YRp-series),self-replicating high copy number (such as the YEp-series), integratingtypes (such as the YIp-series), or mini-chromosomes (such as theYCp-series).

[0083] Higher eukaryotic tissue culture cells are typically thepreferred host cells for expression of the functionally active BS10.55protease or YTF03 oxidoreductase proteins. In principle, many highereukaryotic tissue culture cell lines may be used, e.g., insectbaculovirus expression systems, whether from an invertebrate orvertebrate source. However, mammalian cells are preferred to achieveproper natural processing, both cotranslationally andposttranslationally. Transformation or transfection and propagation ofsuch cells are routine. Useful cell lines include HeLa cells, Chinesehamster ovary (CHO) cell lines, baby rat kidney (BRK) cell lines, insectcell lines, bird cell lines, and monkey (COS) cell lines. Expressionvectors for such cell lines usually include an origin of replication, apromoter, a translation initiation site, RNA splice sites (e.g., ifgenomic DNA is used), a polyadenylation site, and a transcriptiontermination site. These vectors also may contain selection and/oramplification genes. Suitable expression vectors may be plasmids,viruses, or retroviruses carrying promoters derived, e.g., from suchsources as from adenovirus, SV40, parvoviruses, vaccinia virus, orcytomegalovirus. Representative examples of suitable expression vectorsinclude pcDNA1; pCD, see Okayama, et al. (1985) Mol. Cell Biol.5:1136-1142; pMC1neo Poly-A, see Thomas, et al. (1987) Cell 51:503-512;and a baculovirus vector such as pAC 373 or pAC 610.

[0084] It is likely that BS10.55 or YTF03 protein need not beglycosylated to elicit biological responses. However, it willoccasionally be desirable to express a BS10.55 or YTF03 polypeptide in asystem which provides a specific or defined glycosylation pattern. Inthis case, the usual pattern will be that provided naturally by theexpression system. However, the pattern will be modifiable by exposingthe polypeptide, e.g., in unglycosylated form, to appropriateglycosylating proteins introduced into a heterologous expression system.For example, a BS10.55 or YTF03 protein gene may be co-transformed withone or more genes encoding mammalian or other glycosylating enzymes. Itis further understood that over glycosylation may be detrimental toBS10.55 or YTF03 protein biological activity, and that one of skill mayperform routine testing to optimize the degree of glycosylation whichconfers optimal biological activity.

[0085] A BS10.55 or YTF03 protein, or a fragment thereof, may beengineered to be phosphatidyl inositol (PI) linked to a cell membrane,but can be removed from membranes by treatment with a phosphatidylinositol cleaving enzyme, e.g., phosphatidyl inositol phospholipase-C.This releases the antigen in a biologically active form, and allowspurification by standard procedures of protein chemistry. See, e.g., Low(1989) Biochem. Biophys. Acta 988:427-454; Tse, et al. (1985) Science230:1003-1008; and Brunner, et al. (1991) J. Cell Biol. 114:1275-1283.

[0086] Now that BS10.55 or YTF03 proteins have been characterized,fragments or derivatives thereof can be prepared by conventionalprocesses for synthesizing peptides. These include processes such as aredescribed in Stewart and Young (1984) Solid Phase Peptide SynthesisPierce Chemical Co., Rockford, Ill.; Bodanszky and Bodanszky (1984) ThePractice of Peptide Synthesis Springer-Verlag, New York, N.Y.; Bodanszky(1984) The Principles of Peptide Synthesis Springer-Verlag, New York,N.Y.; and Dawson, et al. (1994) Science 266:776-779. For example, anazide process, an acid chloride process, an acid anhydride process, amixed anhydride process, an active ester process (for example,p-nitrophenyl ester, N-hydroxysuccinimide ester, or cyanomethyl ester)ia carbodiimidazole process, an oxidative-reductive process, or adicyclohexylcarbodiimide (DCCD)/additive process can be used. Solidphase and solution phase syntheses are both applicable to the foregoingprocesses.

[0087] The prepared protein and fragments thereof can be isolated andpurified from the reaction mixture by means of peptide separation, forexample, by extraction, precipitation, electrophoresis and various formsof chromatography, and the like. The BS10.55 or YTF03 proteins of thisinvention can be obtained in varying degrees of purity depending uponits desired use. Purification can be accomplished by use of knownprotein purification techniques or by the use of the antibodies orbinding partners herein described, e.g., in immunoabsorbant affinitychromatography. This immunoabsorbant affinity chromatography is carriedout,-e.g., by first linking the antibodies to a solid support and thencontacting the linked antibodies with solubilized lysates of appropriatesource cells, lysates of other cells expressing the ligand, or lysatesor supernatants of cells producing the BS10.55 or YTF03 proteins as aresult of recombinant DNA techniques, see below.

[0088] Multiple cell lines may be screened for one which expresses aBS10.55 or YTF03 polypeptide or protein at a high level compared withother cells. Various cell lines, e.g., a mouse thymic stromal cell lineTA4, is screened and selected for its favorable handling properties.Natural BS10.55 or YTF03 proteins can be isolated from natural sources,or by expression from a transformed cell using an appropriate expressionvector. Purification of the expressed protein is achieved by standardprocedures, or may be combined with engineered means for effectivepurification at high efficiency from cell lysates or supernatants.Epitope or other tags, e.g., FLAG or His₆ segments, can be used for suchpurification features.

[0089] V. Antibodies

[0090] Antibodies can be raised to various BS10.55 or YTF03 proteins,including individual, polymorphic, allelic, strain, or species variants,and fragments thereof, both in their naturally occurring (full-length)forms and in their recombinant forms. Additionally, antibodies can beraised to BS10.55 or YTF03 proteins in either their native (or active)forms or in their inactive, e.g., denatured, forms. Anti-idiotypicantibodies may also be used.

[0091] A. Antibody Production

[0092] A number of immunogens may be used to produce antibodiesspecifically reactive with BS10.55 or YTF03 proteins. Recombinantprotein is a preferred immunogen for the production of monoclonal orpolyclonal antibodies. Naturally occurring protein may also be usedeither in pure or impure form. Synthetic peptides, made using the humanBS10.55 or YTF03 protein sequences described herein, may also used as animmunogen for the production of antibodies to BS10.55 or YTF03 proteins.Recombinant protein can be expressed in eukaryotic or prokaryotic cellsas described herein, and purified as described. Naturally folded ordenatured material can be used, as appropriate, for producingantibodies. Either monoclonal or polyclonal antibodies may be generated,e.g., for subsequent use in immunoassays to measure the protein.

[0093] Methods of producing polyclonal antibodies are well known tothose of skill in the art. Typically, an immunogen, preferably apurified protein, is mixed with an adjuvant and animals are immunizedwith the mixture. The animal's immune response to the immunogenpreparation is monitored by taking test bleeds and determining the titerof reactivity to the BS10.55 or YTF03 protein of interest. For example,when appropriately high titers of antibody to the immunogen areobtained, usually after repeated immunizations, blood is collected fromthe animal and antisera are prepared. Further fractionation of theantisera to enrich for antibodies reactive to the protein can be done ifdesired. See, e.g., Harlow and Lane; or Coligan.

[0094] Monoclonal antibodies may be obtained by various techniquesfamiliar to those skilled in the art. Typically, spleen cells from ananimal immunized with a desired antigen are immortalized, commonly byfusion with a myeloma cell (see, Kohler and Milstein (1976) Eur. J.Immunol. 6:511-519, incorporated herein by reference). Alternativemethods of immortalization include transformation with Epstein BarrVirus, oncogenes, or retroviruses, or other methods known in the art.Colonies arising from single immortalized cells are screened forproduction of antibodies of the desired specificity and affinity for theantigen, and yield of the monoclonal antibodies produced by such cellsmay be enhanced by various techniques, including injection into theperitoneal cavity of a vertebrate host. Alternatively, one may isolateDNA sequences which encode a monoclonal antibody or a binding fragmentthereof by screening a DNA library from human B cells according, e.g.,to the general protocol outlined by Huse, et al. (1989) Science246:1275-1281.

[0095] Antibodies, including binding fragments and single chainversions, against predetermined fragments of BS10.55 or YTF03 proteinscan be raised by immunization of animals with conjugates of thefragments with carrier proteins as described above. Monoclonalantibodies are prepared from cells secreting the desired antibody. Theseantibodies can be screened for binding to normal or defective BS10.55 orYTF03 protein, or screened for agonistic or antagonistic activity, e.g.,mediated through a receptor. These monoclonal antibodies will usuallybind with at least a KD of about 1 mM, more usually at least about 300μM, typically at least about 10 μM, more typically at least about 30 μM,preferably at least about 10 μM, and more preferably at least about 3 μMor better.

[0096] In some instances, it is desirable to prepare monoclonalantibodies from various mammalian hosts, such as mice, rodents,primates, humans, etc. Description of techniques for preparing suchmonoclonal antibodies may be found in, e.g., Stites, et al. (eds.) Basicand Clinical Immunology (4th ed.) Lange Medical Publications, Los Altos,Calif., and references cited therein; Harlow and Lane (1988) Antibodies:A Laboratory Manual CSH Press; Goding (1986) Monoclonal Antibodies:Principles and Practice (2d ed.) Academic Press, New York, N.Y.; andparticularly in Kohler and Milstein (1975) Nature 256:495-497, whichdiscusses one method of generating monoclonal antibodies. Summarizedbriefly, this method involves injecting an animal with an immunogen. Theanimal is then sacrificed and cells taken from its spleen, which arethen fused with myeloma cells. The result is a hybrid cell or“hybridoma” that is capable of reproducing in vitro. The population ofhybridomas is then screened to isolate individual clones, each of whichsecrete a single antibody species to the immunogen. In this manner, theindividual antibody species obtained are the products of immortalizedand cloned single B cells from the immune animal generated in responseto a specific site recognized on the immunogenic substance.

[0097] Other suitable techniques involve selection of libraries ofantibodies in phage or similar vectors. See, e.g., Huse, et al. (1989)“Generation of a Large Combinatorial Library of the ImmunoglobulinRepertoire in Phage Lambda,” Science 246:1275-1281; and Ward, et al.(1989) Nature 341:544-546. The polypeptides and antibodies of thepresent invention may be used with or without modification, includingchimeric or humanized antibodies. Frequently, the polypeptides andantibodies will be labeled by joining, either covalently ornon-covalently, a substance which provides for a detectable signal. Awide variety of labels and conjugation techniques are known and arereported extensively in both the scientific and patent literature.Suitable labels include radionuclides, enzymes, substrates, cofactors,inhibitors, fluorescent moieties, chemiluminescent moieties, magneticparticles, and the like. Patents teaching the use of such labels includeU.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437;4,275,149; and 4,366,241. Also, recombinant immunoglobulins may beproduced, see, Cabilly, U.S. Pat. No. 4,816,567; and Queen, et al.(1989) Proc. Nat'l Acad. Sci. USA 86:10029-10033; or made in transgenicmice, see Mendez, et al. (1997) Nature Genetics 15:146-156.

[0098] The antibodies of this invention are useful for affinitychromatography in isolating BS10.55 or YTF03 protein. Columns can beprepared where the antibodies are linked to a solid support, e.g.,particles, such as agarose, SEPHADEX, or the like, where a cell lysateor supernatant may be passed through the column, the column washed,followed by increasing concentrations of a mild denaturant, wherebypurified BS10.55 or YTF03 protein will be released. The converse can beperformed using protein to isolate specific antibodies.

[0099] Other antibodies may block enzymatic activity. The antibodies mayalso be used to screen expression libraries for particular expressionproducts. Usually the antibodies used in such a procedure will belabeled with a moiety allowing easy detection of presence of antigen byantibody binding.

[0100] Antibodies to BS10.55 or YTF03 proteins may be used for theidentification of cell populations expressing BS10.55 or YTF03 protein.By assaying the expression products of cells expressing BS10.55 or YTF03proteins it is possible to diagnose disease, e.g., metabolic conditions.The proteins may also be markers for specific tissue or cellsubpopulations, e.g., dendritic cells.

[0101] Antibodies raised against each BS10.55 or YTF03 protein will alsobe useful to raise anti-idiotypic antibodies. These will be useful indetecting or diagnosing various immunological conditions related toexpression of the respective antigens.

[0102] B. Immunoassays

[0103] A particular protein can be measured by a variety of immunoassaymethods. For a review of immunological and immunoassay procedures ingeneral, see Stites and Terr (eds.) (1991) Basic and Clinical Immunology(7th ed.). Moreover, the immunoassays of the present invention can beperformed in many configurations, which are reviewed extensively inMaggio (ed.) (1980) Enzyme Immunoassay CRC Press, Boca Raton, Fla.;Tijan (1985) “Practice and Theory of Enzyme Immunoassays,” LaboratoryTechniaues in Biochemistry and Molecular Biology, Elsevier SciencePublishers B. V., Amsterdam; and Harlow and Lane Antibodies. ALaboratory Manual, supra, each of which is incorporated herein byreference. See also Chan (ed. 1987) Immunoassay: A Practical GuideAcademic Press, Orlando, Fla.; Price and Newman (eds. 1991) Principlesand Practice of Immunoassays Stockton Press, NY; and Ngo (ed. 1988)Non-isotopic Immunoassays Plenum Press, NY.

[0104] Immunoassays for measurement of BS10.55 or YTF03 proteins orpeptides can be performed by a variety of methods known to those skilledin the art. In brief, immunoassays to measure the protein can be eithercompetitive or noncompetitive binding assays. In competitive bindingassays, the sample to be analyzed competes with a labeled analyte forspecific binding sites on a capture agent bound to a solid surface.Preferably the capture agent is an antibody specifically reactive withBS10.55 or YTF03 proteins produced as described above. The concentrationof labeled analyte bound to the capture agent is inversely proportionalto the amount of free analyte present in the sample.

[0105] In a competitive binding immunoassay, the BS10.55 or YTF03protein present in the sample competes with labeled protein for bindingto a specific binding agent, for example, an antibody specificallyreactive with the BS10.55 or YTF03 protein. The binding agent may bebound to a solid surface to effect separation of bound labeled proteinfrom the unbound labeled protein. Alternately, the competitive bindingassay may be conducted in liquid phase and a variety of techniques knownin the art may be used to separate the bound labelled protein from theunbound labeled protein. Following separation, the amount of boundlabeled protein is determined. The amount of protein present in thesample is inversely proportional to the amount of labeled proteinbinding.

[0106] Alternatively, a homogeneous-immunoassay may be performed inwhich a separation step is not needed. In these immunoassays, the labelon the protein is altered by the binding of the protein to its specificbinding agent. This alteration in the labeled protein results in adecrease or increase in the signal emitted by label, so that measurementof the label at the end of the immunoassay allows for detection orquantitation of the protein.

[0107] BS10.55 or YTF03 proteins may also be determined by a variety ofnoncompetitive immunoassay methods. For example, a two-site, solid phasesandwich immunoassay may be used. In this type of assay, a binding agentfor the protein, for example an antibody, is attached to a solidsupport. A second protein binding agent, which may also be an antibody,and which binds the protein at a different site, is labeled. Afterbinding at both sites on the protein has occurred, the unbound labeledbinding agent is removed and the amount of labeled binding agent boundto the solid phase is measured. The amount of labeled binding agentbound is directly proportional to the amount of protein in the sample.

[0108] Western blot analysis can be used to determine the presence ofBS10.55 or YTF03 proteins in a sample. Electrophoresis is carried out,for example, on a tissue sample suspected of containing the protein.Following electrophoresis to separate the proteins, and transfer of theproteins to a suitable solid support, e.g., a nitrocellulose filter, thesolid support is incubated with an antibody reactive with the protein.This antibody may be labeled, or alternatively may be detected bysubsequent incubation with a second labeled antibody that binds theprimary antibody.

[0109] The immunoassay formats described above may employ labeled assaycomponents. The label may be coupled directly or indirectly to thedesired component of the assay according to methods well known in theart. A wide variety of labels and methods may be used. Traditionally, aradioactive label incorporating ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²P was used.Non-radioactive labels include ligands which bind to labeled antibodies,fluorophores, chemiluminescent agents, enzymes, and antibodies which canserve as specific binding pair members for a labeled ligand. The choiceof label depends on sensitivity required, ease of conjugation with thecompound, stability requirements, and available instrumentation. For areview of various labeling or signal producing systems which may beused, see U.S. Pat. No. 4,391,904, which is incorporated herein byreference.

[0110] Antibodies reactive with a particular protein can also bemeasured by a variety of immunoassay methods. For a review ofimmunological and immunoassay procedures applicable to the measurementof antibodies by immunoassay techniques, see Stites and Terr (eds.)Basic and Clinical Immunology (7th ed.) supra; Maggio (ed.) EnzymeImmunoassay, supra; and Harlow and Lane Antibodies. A Laboratory Manual,supra.

[0111] In brief, immunoassays to measure antisera reactive with BS10.55or YTF03 proteins can be either competitive or noncompetitive bindingassays. In competitive binding assays, the sample analyte competes witha labeled analyte for specific binding sites on a capture agent bound toa solid surface. Preferably the capture agent is a purified recombinantBS10.55 or YTF03 protein produced as described above. Other sources ofBS10.55 or YTF03 proteins, including isolated or partially purifiednaturally occurring protein, may also be used. Noncompetitive assaysinclude sandwich assays, in which the sample analyte is bound betweentwo analyte-specific binding reagents. One of the binding agents is usedas a capture agent and is bound to a solid surface. The second bindingagent is labeled and is used to measure or detect the resultant complexby visual or instrument means. A number of combinations of capture agentand labelled binding agent can be used. A variety of differentimmunoassay formats, separation techniques, and labels can be also beused similar to those described above for the measurement of BS10.55 orYTF03 proteins. Similar methods may be used to evaluate or quantitatespecific binding compounds.

[0112] VI. Purified BS10.55 or YTF03 Proteins

[0113] Human BS10.55 or YTF03 protein amino acid sequences are providedin SEQ ID NQ: 2 and 4.

[0114] Purified protein or defined peptides are useful for generatingantibodies by standard methods, as described above. Synthetic peptidesor purified protein can be presented to an immune system to generatepolyclonal and monoclonal antibodies. See, e.g., Coligan (1991) CurrentProtocols in Immunology Wiley/Greene, NY; and Harlow and Lane (1989)Antibodies: A Laboratory Manual Cold Spring Harbor Press, NY, which areincorporated herein by reference.

[0115] The specific binding composition can be used for screening anexpression library made from a cell line which expresses a BS10.55 orYTF03 protein. Many methods for screening are available, e.g., standardstaining of surface expressed ligand, or by panning. Screening ofintracellular expression can also be performed by various staining orimmunofluorescence procedures. The binding compositions could be used toaffinity purify or sort out cells expressing the ligand.

[0116] The peptide segments, along with comparison to homologous genes,can also be used to produce appropriate oligonucleotides to screen alibrary. The genetic code can be used to select appropriateoligonucleotides useful as probes for screening. In combination withpolymerase chain reaction (PCR) techniques, synthetic oligonucleotideswill be useful in selecting desired clones from a library, includingnatural allelic and polymorphic variants.

[0117] The peptide sequences allow preparation of peptides to generateantibodies to recognize such segments, and allow preparation ofoligonucleotides which encode such sequences. The sequence also allowsfor synthetic preparation, e.g., see Dawson, et al. (1994) Science266:776-779. Analysis of the structural features in comparison with themost closely related reported sequences has revealed similarities withother proteins, particularly the class of proteins known as proteases oroxidoreductases.

[0118] VII. Physical Variants

[0119] This invention also encompasses proteins or peptides havingsubstantial amino acid sequence similarity with an amino acid sequenceof a BS10.55 or YTF03 protein. Natural variants include individual,polymorphic, allelic, strain, or species variants. Conservativesubstitutions in the amino acid sequence will normally preserve mostrelevant biological activities. In particular, various substitutions canbe made, e.g., embodiments with 10-fold substitutions, 7-foldsubstitutions, 5-fold substitutions, 3-fold substitutions, 2-fold, andetc. Such embodiments will typically retain particular features, e.g.,antigenicity, with the natural forms.

[0120] Amino acid sequence similarity, or sequence identity, isdetermined by optimizing residue matches, if necessary, by introducinggaps as required. This changes when considering conservativesubstitutions as matches. Conservative substitutions typically includesubstitutions within the following groups: glycine, alanine; valine,isoleucine, leucine; aspartic acid, glutamic acid; asparagine,glutamine; serine, threonine; lysine, arginine; and phenylalanine,tyrosine. Homologous amino acid sequences include natural polymorphic,allelic, and interspecies variations in each respective proteinsequence. Typical homologous proteins or peptides will have from 50-100%similarity (if gaps can be introduced), to 75-100% similarity (ifconservative substitutions are included) with the amino acid sequence ofthe BS10.55 or YTF03 protein. Similarity measures will be at least about50%, generally at least about 60%, more generally at least about 65%,usually at least about 70%, more usually at least about 75%, preferablyat least about 80%, and more preferably at least about 80%, and inparticularly preferred embodiments, at least about 85% or more. See alsoNeedleham, et al. (1970) J. Mol. Biol. 48:443-453; Sankoff, et al.(1983) Time Warps, String Edits and Macromolecules: The Theory andPractice of Sequence Comparison Chapter One, Addison-Wesley, Reading,Mass.; and software packages from IntelliGenetics, Mountain View,Calif.; and the University of Wisconsin Genetics Computer Group,Madison, Wis.

[0121] Natural nucleic acids encoding mammalian BS10.55 or YTF03proteins will typically hybridize to the nucleic acid sequence of SEQ IDNO: 1 or 3 under stringent conditions. For example, nucleic acidsencoding human BS10.55 or YTF03 proteins will normally hybridize to thenucleic acid of SEQ ID NO: 1 or 3 under stringent hybridizationconditions. Generally, stringent conditions are selected to be about 10°C. lower than the thermal melting point (Tm) for the probe sequence at adefined ionic strength and pH. The Tm is the temperature (under definedionic strength and pH) at which 50% of the target sequence hybridizes toa perfectly matched probe. Typically, stringent conditions will be thosein which the salt concentration is about 0.2 molar at pH 7 and thetemperature is at least about 50° C. Other factors may significantlyaffect the stringency of hybridization, including, among others, basecomposition and size of the complementary strands, the presence oforganic solvents such as formamide, and the extent of base mismatching.A preferred embodiment will include nucleic acids which will bind todisclosed sequences in 50% formamide and 200 mM NaCl at 42° C. See,e.g., Sambrook, et al.

[0122] An isolated BS10.55 or YTF03 protein DNA can be readily modifiedby nucleotide substitutions, nucleotide deletions, nucleotideinsertions, and short inversions of nucleotide stretches. Thesemodifications result in novel DNA sequences which encode BS10.55 orYTF03 protein antigens, their derivatives, or proteins having highlysimilar physiological, immunogenic, or antigenic activity.

[0123] Modified sequences can be used to produce mutant antigens or toenhance expression. Enhanced expression may involve gene amplification,increased transcription, increased translation, and other mechanisms.Such mutant BS10.55 or YTF03 protein derivatives include predeterminedor site-specific mutations of the respective protein or its fragments.“Mutant BS10.55 or YTF03 protein” encompasses a polypeptide otherwisefalling within the homology definition of the human BS10.55 or YTF03protein as set forth above, but having an amino acid sequence whichdiffers from that of a BS10.55 or YTF03 protein as found in nature,whether by way of deletion, substitution, or insertion. In particular,“site specific mutant BS10.55 or YTF03 protein” generally includesproteins having significant similarity with a protein having a sequenceof SEQ ID NO: 2 or 4, and as sharing various biological activities,e.g., antigenic or immunogenic, with those sequences, and in preferredembodiments contain most or all of the disclosed sequence. This appliesalso to polymorphic variants from different individuals. Similarconcepts apply to different BS10.55 or YTF03 proteins, particularlythose found in various warm blooded animals, e.g., mammals and birds. Asstated before, it is emphasized that descriptions are generally meant toencompass other BS10.55 or YTF03 proteins, not limited to the humanembodiments specifically discussed.

[0124] Although site specific mutation sites are predetermined, mutantsneed not be site specific. BS10.55 or YTF03 protein mutagenesis can beconducted by making amino acid insertions or deletions. Substitutions,deletions, insertions, or combinations may be generated to arrive at afinal construct. Insertions include amino- or carboxyl terminal fusions,e.g. epitope tags. Random mutagenesis can be conducted at a target codonand the expressed mutants can then be screened for the desired activity.Methods for making substitution mutations at predetermined sites in DNAhaving a known sequence are well known in the art, e.g., by M13 primermutagenesis or polymerase chain reaction (PCR) techniques. See also,Sambrook, et al. (1989) and Ausubel, et al. (1987 and Supplements). Themutations in the DNA normally should not place coding sequences out ofreading frames and preferably will not create complementary regions thatcould hybridize to produce secondary mRNA structure such as loops orhairpins.

[0125] The present invention also provides recombinant proteins, e.g.,heterologous fusion proteins using segments from these proteins. Aheterologous fusion protein is a fusion of proteins or segments whichare naturally not normally fused in the same manner. Thus, the fusionproduct of an immunoglobulin with a BS10.55 or YTF03 protein polypeptideis a continuous protein molecule having sequences fused in a typicalpeptide linkage, typically made as a single translation product andexhibiting properties derived from each source peptide. A similarconcept applies to heterologous nucleic acid sequences. Antibody fusionproteins are also contemplated.

[0126] In addition, new constructs may be made from combining similarfunctional domains from other proteins. For example, protein-binding orother segments may be “swapped” between different new fusionpolypeptides or fragments. See, e.g., Cunningham, et al. (1989) Science243:1330-1336; and O'Dowd, et al. (1988) J. Biol. Chem. 263:15985-15992.Thus, new chimeric polypeptides exhibiting new combinations ofspecificities will result from the functional linkage of protein-bindingspecificities and other functional domains.

[0127] VIII. Binding Agent:BS10.55 or Agent:YTF03 Protein Complexes

[0128] A BS10.55 or YTF03 protein that specifically binds to or that isspecifically immunoreactive with an antibody generated against a definedimmunogen, such as an immunogen consisting of the amino acid sequence ofSEQ ID NO: 2 or 4, is typically determined in an immunoassay. Theimmunoassay uses a polyclonal antiserum which was raised to a protein ofSEQ ID NO: 2 or 4. This antiserum is selected to have lowcrossreactivity against other proteases and any such crossreactivity isremoved by immunoabsorption prior to use in the immunoassay.

[0129] In order to produce antisera for use in an immunoassay, theprotein of SEQ ID NO: 2 or 4 is isolated as described herein. Forexample, recombinant protein may be produced in a mammalian cell line.An inbred strain of mice such as balb/c is immunized with the protein ofSEQ ID NO: 2 or 4 using a standard adjuvant, such as Freund's adjuvant,and a standard mouse immunization protocol (see Harlow and Lane, supra).Alternatively, a synthetic peptide, preferably near full length, derivedfrom the sequences disclosed herein and conjugated to a carrier proteincan be used an immunogen. Polyclonal sera are collected and titeredagainst the immunogen protein in an immunoassay, for example, a solidphase immunoassay with the immunogen immobilized on a solid support.Polyclonal antisera with a titer of 104 or greater are selected andtested for their cross reactivity against other proteases oroxidoreductases, e.g., using a competitive binding immunoassay such asthe one described in Harlow and Lane, supra, at pages 570-573.Preferably two related proteins are used in this determination inconjunction with either BS10.55 or YTF03 protein.

[0130] Immunoassays in the competitive binding format can be used forthe crossreactivity determinations. For example, a protein of SEQ ID NO:2 or 4 can be immobilized to a solid support. Proteins added to theassay compete with the binding of the antisera to the immobilizedantigen. The ability of the above proteins to compete with the bindingof the antisera to the immobilized protein is compared to the protein ofSEQ ID NO: 2 or 4. The percent crossreactivity for the above proteins iscalculated, using standard calculations. Those antisera with less than10% crossreactivity with each of the proteins listed above are selectedand pooled. The cross-reacting antibodies are then removed from thepooled antisera by immunoabsorbtion with the above-listed proteins.

[0131] The immunoabsorbed and pooled antisera are then used in acompetitive binding immunoassay as described above to compare a secondprotein to the immunogen protein (e.g., the protein motif of SEQ ID NO:2 or 4). In order to make this comparison, the two proteins are eachassayed at a wide range of concentrations and the amount of each proteinrequired to inhibit 50% of the binding of the antisera to theimmobilized protein is determined. If the amount of the second proteinrequired is less than twice the amount of the protein of SEQ ID NO: 2 or4 that is required, then the second protein is said to specifically bindto an antibody generated to the immunogen.

[0132] It is understood that BS10.55 or YTF03 proteins are families ofhomologous proteins that comprise two or more genes. For a particulargene product, such as the human BS10.55 or YTF03 proteins, the termrefers not only to the amino acid sequences disclosed herein, but alsoto other proteins that are polymorphic, allelic, non-allelic, or speciesvariants or equivalents. It is also understood that the term “humanBS10.55 or YTF03 protein” includes equivalent proteins, e.g., nonnaturalmutations introduced by deliberate mutation using conventionalrecombinant technology such as single site mutation, or by excisingshort sections of DNA encoding BS10.55 or YTF03 proteins, or bysubstituting new amino acids, or adding new amino acids. Such minoralterations must substantially maintain the immunoidentity of theoriginal molecule and/or its biological activity. Thus, thesealterations include proteins that are specifically immunoreactive with adesignated naturally occurring BS10.55 or YTF03 protein, for example,the human BS10.55 or YTF03 protein shown in SEQ ID NO: 2 or 4. Thebiological properties of the altered proteins can be determined byexpressing the protein in an appropriate cell line and measuring, e.g.,enzymatic activity uncer appropriate conditions. Particular proteinmodifications considered minor would include conservative substitutionof amino acids with similar chemical properties, as described above forBS10.55 or YTF03 protein families as a whole. By aligning a proteinoptimally with the protein of SEQ ID NO: 2 or 4, and by using theconventional immunoassays described herein to determine immunoidentity,or by using lymphocyte chemotaxis assays, one can determine the proteincompositions of the invention.

[0133] IX. Functional Variants

[0134] The blocking of physiological response to BS10.55 or YTF03protein may result from the inhibition of enzymatic activity of theprotein against its substrate, e.g., through competitive inhibition.Thus, in vitro assays of the present invention will often use isolatedprotein, membranes from cells expressing a recombinant membraneassociated proteins, soluble fragments comprising enzymatically activesegments of these proteins, or fragments attached to solid phasesubstrates. These assays will also allow for the diagnosticdetermination of the effects of either binding segment mutations andmodifications, or protein mutations and modifications, e.g., proteinanalogs. This invention also contemplates the use of competitive drugscreening assays, e.g., where neutralizing antibodies to antigen orenzyme fragments compete with a test compound for binding to theprotein. In this manner, the antibodies can be used to detect thepresence of a polypeptide which shares one or more antigenic bindingsites of the protein and can also be used to occupy binding sites on theprotein that might otherwise interact with, e.g., substrate.

[0135] “Derivatives” of BS10.55 or YTF03 proteins include amino acidsequence mutants, glycosylation variants, and covalent or aggregateconjugates with other chemical moieties. Covalent derivatives can beprepared by linkage of functionalities to groups which are found inBS10.55 or YTF03 protein amino acid side chains or at the N- orC-termini, e.g., by means which are well known in the art. Thesederivatives can include, without limitation, aliphatic esters or amidesof the carboxyl terminus, or of residues containing carboxyl sidechains, O-acyl derivatives of hydroxyl group-containing residues, andN-acyl derivatives of the amino terminal amino acid or amino-groupcontaining residues, e.g., lysine or arginine. Acyl groups are typicallyselected from the group of alkyl-moieties including C3 to C18 normalalkyl, thereby forming alkanoyl aroyl species. Covalent attachment tocarrier proteins may be important when immunogenic moieties are haptens.

[0136] In particular, glycosylation alterations are included, e.g., madeby modifying the glycosylation patterns of a polypeptide during itssynthesis and processing, or in further processing steps. Particularlypreferred means for accomplishing this are by exposing the polypeptideto glycosylating enzymes derived from cells which normally provide suchprocessing, e.g., mammalian glycosylation enzymes. Deglycosylationenzymes are also contemplated. Also embraced are versions of the sameprimary amino acid sequence which have other minor modifications,including phosphorylated amino acid residues, e.g., phosphotyrosine,phosphoserine, or phosphothreonine, or other moieties, including ribosylgroups or cross-linking reagents.

[0137] A major group of derivatives are covalent conjugates of theBS10.55 or YTF03 protein or fragments thereof with other proteins orpolypeptides. These derivatives can be synthesized in recombinantculture such as N- or C-terminal fusions or by the use of agents knownin the art for their usefulness in cross-linking proteins throughreactive side groups. Preferred protein derivatization sites withcross-linking agents are at free amino groups, carbohydrate moieties,and cysteine residues.

[0138] Fusion polypeptides between human BS10.55 or YTF03 proteins andother homologous or heterologous proteins are also provided.Heterologous polypeptides may be fusions between different relatedproteins, resulting in, e.g., a hybrid protein exhibiting modifiedsubstrate or other binding specificity. Likewise, heterologous fusionsmay be constructed which would exhibit a combination of properties oractivities of the derivative proteins. Typical examples are fusions of areporter polypeptide, e.g., luciferase, with a segment or domain of aprotein, e.g., a receptor-binding segment, so that the presence orlocation of the fused protein may be easily determined. See, e.g., Dull,et al., U.S. Pat. No. 4,859,609. Other gene fusion partners includebacterial β-galactosidase, trpE, Protein A, β-lactamase, alpha amylase,alcohol dehydrogenase, and yeast alpha mating factor. See, e.g.,Godowski, et al. (1988) Science 241:812-816.

[0139] Such polypeptides may also have amino acid residues which havebeen chemically modified by phosphorylation, sulfonation, biotinylation,or the addition or removal of other moieties, particularly those whichhave molecular shapes similar to phosphate groups. In some embodiments,the modifications will be useful labeling reagents, or serve aspurification targets, e.g., affinity ligands.

[0140] This invention also contemplates the use of derivatives ofBS10.55 or YTF03 proteins other than variations in amino acid sequenceor glycosylation. Such derivatives may involve covalent or aggregativeassociation with chemical moieties. These derivatives generally includethe three classes: (1) salts, (2) side chain and terminal residuecovalent modifications, and (3) adsorption complexes, for example withcell membranes. Such covalent or aggregative derivatives are useful asimmunogens, as reagents in immunoassays, or in purification methods suchas for affinity purification of ligands or other binding ligands. Forexample, a BS10.55 or YTF03 protein can be immobilized by covalentbonding to a solid support such as cyanogen bromide-activated SEPHAROSE,by methods which are well known in the art, or adsorbed onto polyolefinsurfaces, with or without glutaraldehyde cross-linking, for use in theassay or purification of anti-BS10.55 or anti-YTF03 protein antibodies.The BS10.55 or YTF03 proteins can also be labeled with a detectablegroup, e.g., radioiodinated by the chloramine T procedure, covalentlybound to rare earth chelates, or conjugated to another fluorescentmoiety for use in diagnostic assays. Purification of BS10.55 or YTF03proteins may be effected by immobilized antibodies or substrate.

[0141] Isolated BS10.55 or YTF03 protein genes will allow transformationof cells lacking expression of corresponding BS10.55 or YTF03 proteins,e.g., either species types or cells which lack corresponding proteinsand exhibit negative background activity. Expression of transformedgenes will allow isolation of antigenically pure cell lines, withdefined or single specie variants. This approach will allow for moresensitive detection and discrimination of the physiological effects ofBS10.55 or YTF03 protein substrate proteins. Subcellular fragments,e.g., cytoplasts or membrane fragments, can be isolated and used.

[0142] X. Uses

[0143] The present invention provides reagents which will find use indiagnostic applications as described elsewhere herein, e.g., in thegeneral description for metabolic abnormalities, or below in thedescription of kits for diagnosis.

[0144] BS10.55 or YTF03 protein nucleotides, e.g., human BS10.55 orYTF03 protein DNA or RNA, may be used as a component in a forensicassay. For instance, the nucleotide sequences provided may be labeledusing, e.g., ³²P or biotin and used to probe standard restrictionfragment polymorphism blots, providing a measurable character to aid indistinguishing between individuals. Such probes may be used inwell-known forensic techniques such as genetic fingerprinting. Inaddition, nucleotide probes made from BS10.55 or YTF03 protein sequencesmay be used in in situ assays to detect chromosomal abnormalities.

[0145] Antibodies and other binding agents directed towards BS10.55 orYTF03 proteins or nucleic acids may be used to purify the correspondingBS10.55 or YTF03 protein molecule. As described in the Examples below,antibody purification of BS10.55 or YTF03 protein components is bothpossible and practicable. Antibodies and other binding agents may alsobe used in a diagnostic fashion to determine whether BS10.55 or YTF03protein components are present in a tissue sample or cell populationusing well-known techniques described herein. The ability to attach abinding agent to a BS10.55 or YTF03 protein provides a means to diagnosedisorders associated with BS10.55 or YTF03 protein misregulation.Antibodies and other BS10.55 or YTF03 protein binding agents may also beuseful as histological or sorting markers. As described in the examplesbelow, BS10.55 or YTF03 protein expression is limited to specific tissuetypes. By directing a probe, such as an antibody or nucleic acid to aBS10.55 or YTF03 protein, it is possible to use the probe to distinguishtissue and cell types in situ or in vitro.

[0146] This invention also provides reagents with significanttherapeutic value. The BS10.55 or YTF03 protein (naturally occurring orrecombinant), fragments thereof, and antibodies thereto, along withcompounds identified as having binding affinity to a BS10.55 or YTF03protein, are useful in the treatment of conditions associated withabnormal metabolism, physiology, or development, including abnormalimmune responsiveness or non-responsiveness. Abnormal proliferation,regeneration, degeneration, and atrophy may be modulated by appropriatetherapeutic treatment using the compositions provided herein. TheBS10.55 or YTF03 proteins likely play roles in regulation or developmentof hematopoietic cells, e.g., lymphoid cells, which affect immunologicalresponses. Thus, for example, an antagonist of a BS10.55 or YTF03protein could be useful in blocking the conversion of an immature orinactive immunologically relevant pro-protein to the mature or activeform. Since the BS10.55 proteases were derived from dendritic cells,antagonists could also be important in preventing antigen processingand/or subsequent presentation.

[0147] Other abnormal developmental conditions are known in cell typesshown to possess BS10.55 or YTF03 protein encoding mRNA by northern blotanalysis. See Berkow (ed.) The Merck Manual of Diagnosis and Therapy,Merck & Co., Rahway, N.J.; and Thorn, et al. Harrison s Principles ofInternal Medicine, McGraw-Hill, N.Y. Developmental or functionalabnormalities, e.g., of the immune system, cause significant medicalabnormalities and conditions which may be susceptible to prevention ortreatment using compositions provided herein.

[0148] Recombinant BS10.55 or YTF03 protein antibodies can be purifiedand then administered to a patient. These reagents can be combined fortherapeutic use with additional active or inert ingredients, e.g., inconventional pharmaceutically acceptable carriers or diluents, e.g.,immunogenic adjuvants, along with physiologically innocuous stabilizersand excipients. These combinations can be sterile filtered and placedinto dosage forms as by lyophilization in dosage vials or storage instabilized aqueous preparations. This invention also contemplates use ofantibodies or binding fragments thereof, including forms which are notcomplement binding.

[0149] Drug screening using antibodies or fragments thereof can identifycompounds having binding affinity to BS10.55 or YTF03 protein, includingisolation of associated components. Various substrate candidates can bescreened. Subsequent biological assays can then be utilized to determineif the compound has intrinsic enzyme blocking activity. Likewise, acompound having intrinsic stimulating activity might activate theactivity of a BS10.55 or YTF03 protein. This invention furthercontemplates the therapeutic use of antibodies to BS10.55 or YTF03protein as antagonists. This approach should be particularly useful withother BS10.55 or YTF03 protein polymorphic or species variants.

[0150] The quantities of reagents necessary for effective therapy willdepend upon many different factors, including means of administration,target site, physiological state of the patient, and other medicantsadministered. Thus, treatment dosages should be titrated to optimizesafety and efficacy. Typically, dosages used in vitro may provide usefulguidance in the amounts useful for in situ administration of thesereagents. Animal testing of effective doses for treatment of particulardisorders will provide further predictive indication of human dosage.Various considerations are described, e.g., in Gilman, et al. (eds.)(1990) Goodman and Gilman's: The Pharmacological Bases of Therapeutics(8th ed.) Pergamon Press; and (1990) Remington's Pharmaceutical Sciences(17th ed.) Mack Publishing Co., Easton, Pa. Methods for administrationare discussed therein and below, e.g., for oral, intravenous,intraperitoneal, or intramuscular administration, transdermal diffusion,and others. Pharmaceutically acceptable carriers will include water,saline, buffers, and other compounds described, e.g., in the MerckIndex, Merck & Co., Rahway, N.J. Dosage ranges would ordinarily beexpected to be in amounts lower than 1 mM concentrations, typically lessthan about 10 μM concentrations, usually less than about 100 nM,preferably less than about 10 pM (picomolar), and most preferably lessthan about 1 fM (femtomolar), with an appropriate carrier. Slow releaseformulations, or a slow release apparatus will often be utilized forcontinuous administration.

[0151] BS10.55 or YTF03 proteins, fragments thereof; antibodies to it orits fragments; antagonists; and agonists, may be administered directlyto the host to be treated or, depending on the size of the compounds, itmay be desirable to conjugate them to carrier proteins such as ovalbuminor serum albumin prior to their administration. Therapeutic formulationsmay be administered in any conventional dosage formulation. While it ispossible for the active ingredient to be administered alone, it ispreferable to present it as a pharmaceutical formulation. Formulationstypically comprise at least one active ingredient, as defined above,together with one or more acceptable carriers thereof. Each carriershould be both pharmaceutically and physiologically acceptable in thesense of being compatible with the other ingredients and not injuriousto the patient. Formulations include those suitable for oral, rectal,nasal, or parenteral (including subcutaneous, intramuscular, intravenousand intradermal) administration. The formulations may conveniently bepresented in unit dosage form and may be prepared by any methods wellknown in the art of pharmacy. See, e.g., Gilman, et al. (eds.) (1990)Goodman and Gilman's: The Pharmacological Bases of Therapeutics (8thed.) Pergamon Press; and (1990) Remington's Pharmaceutical Sciences(17th ed.) Mack Publishing Co., Easton, Pa.; Avis, et al. (eds.) (1993)Pharmaceutical Dosage Forms: Parenteral Medications Dekker, NY;Lieberman, et al. (eds.) (1990) Pharmaceutical Dosage Forms: TabletsDekker, NY; and Lieberman, et al. (eds.) (1990) Pharmaceutical DosageForms: Disperse Systems Dekker, NY. The therapy of this invention may becombined with or used in association with other therapeutic agents.

[0152] Both the naturally occurring and the recombinant forms of theBS10.55 or YTF03 proteins of this invention are particularly useful inkits and assay methods which are capable of screening compounds forbinding activity to the proteins, including substrates or competitiveinhibitors. Several methods of automating assays have been developed inrecent years so as to permit screening of tens of thousands of compoundsin a short period. See, e.g., Fodor, et al. (1991) Science 251:767-773,and other descriptions of chemical diversity libraries, which describemeans for testing of binding affinity by a plurality of compounds. Thedevelopment of suitable assays can be greatly facilitated by theavailability of large amounts of purified, soluble BS10.55 or YTF03protein as provided by this invention.

[0153] For example, antagonists can normally be found once the proteinhas been structurally defined. Testing of potential substrates oranalogs is now possible upon the development of highly automated assaymethods using a purified enzyme. In particular, new agonists andantagonists will be discovered by using screening techniques describedherein. Of particular importance are compounds found to have a combinedblockage activity for multiple BS10.55 or YTF03 protein substrates,e.g., compounds which can serve as antagonists for polymorphic orspecies variants of a BS10.55 or YTF03 protein.

[0154] This invention is particularly useful for screening compounds byusing recombinant protein in a variety of drug screening techniques. Theadvantages of using a recombinant protein in screening for specificligands include: (a) improved renewable source of the BS10.55 or YTF03protein from a specific source; (b) potentially greater number ofmolecules per cell giving better signal to noise ratio in assays; and(c) species variant specificity (theoretically giving greater biologicaland disease specificity).

[0155] One method of drug screening utilizes eukaryotic or prokaryotichost cells which are stably transformed with recombinant DNA moleculesexpressing a BS10.55 or YTF03 protein substrate. Cells may be isolatedwhich express a substrate in isolation from any others. Such cells,either in viable or fixed form, can be used for standardenzyme/substrate cleavage or oxidoreductase assays. See also, Parce, etal. (1989) Science 246:243-247; and Owicki, et al. (1990) Proc. Nat'lAcad. Sci, USA 87:4007-4011, which describe sensitive methods to detectcellular responses. Competitive assays are particularly useful, wherethe cells (source of BS10.55 or YTF03 protein) or homogenates arecontacted and incubated with a labeled antibody having known bindingaffinity to the protein, such as ¹²⁵I-antibody, and a test sample whosebinding affinity to the binding composition is being measured. The boundand free labeled binding compositions are then separated to assess thedegree of antigen binding. The amount of test compound bound isinversely proportional to the amount of labeled reagent binding to theknown source. Any one of numerous techniques can be used to separatebound from free antigen to assess the degree of ligand binding. Thisseparation step could typically involve a procedure such as adhesion tofilters followed by washing, adhesion to plastic followed by washing, orcentrifugation of the cell membranes. Viable cells could also be used toscreen for the effects of drugs on BS10.55 or YTF03 protein mediatedfunctions, e.g., substrate cleavage, oxidoreductase activity, andothers. Some detection methods allow for elimination of a separationstep, e.g., a proximity sensitive detection system.

[0156] Another method utilizes solubilized, unpurified or solubilized,purified BS10.55 or YTF03 protein from transformed eukaryotic orprokaryotic host cells. This allows for a “molecular” binding assay withthe advantages of increased specificity, the ability to automate, andhigh drug test throughput.

[0157] Another technique for drug screening involves an approach whichprovides high throughput screening for compounds having suitable bindingaffinity to a BS10.55 or YTF03 protein, e.g., an antibody, is describedin detail in Geysen, European Patent Application 84/03564, published onSep. 13, 1984. First, large numbers of different small peptide testcompounds are synthesized on a solid substrate, e.g., plastic pins orsome other appropriate surface, see Fodor, et al., supra. Then all thepins are reacted with solubilized, unpurified or solubilized, purifiedBS10.55 or YTF03 protein antibody, and washed. The next step involvesdetecting bound BS10.55 or YTF03 protein antibody.

[0158] Rational drug design may also be based upon structural studies ofthe molecular shapes of the BS10.55 or YTF03 protein and other effectorsor analogs. See, e.g., Methods in Enzymology vols 202 and 203. Effectorsmay be other proteins which mediate other functions in response toantigen binding, or other proteins which normally interact with thesubstrate. One means for determining which sites interact with specificother proteins is a physical structure determination, e.g., x-raycrystallography or 2 dimensional NMR techniques. These will provideguidance as to which amino acid residues form molecular contact regions.For a detailed description of protein structural determination, see,e.g., Blundell and Johnson (1976) Protein Crystallography AcademicPress, NY.

[0159] A purified BS10.55 or YTF03 protein can be coated directly ontoplates for use in the aforementioned drug screening techniques. However,non-neutralizing antibodies to these antigens can be used as captureantibodies to immobilize the respective antigen on the solid phase.

[0160] XI. Kits

[0161] This invention also contemplates use of BS10.55 or YTF03proteins, fragments thereof, peptides, and their fusion products in avariety of diagnostic kits and methods for detecting the presence ofBS10.55 or YTF03 protein or a BS10.55 or YTF03 protein substrate.Typically the kit will have a compartment containing either a definedBS10.55 or YTF03 peptide or gene segment or a reagent which recognizesone or the other, e.g., substrates or antibodies.

[0162] A kit for determining the binding affinity of a test compound toa BS10.55 or YTF03 protein would typically comprise a test compound; alabeled compound, e.g., an antibody having known binding affinity forthe BS10.55 or YTF03 protein; a source of BS10.55 or YTF03 protein(naturally occurring or recombinant); and a means for separating boundfrom free labeled compound, such as a solid phase for immobilizing theBS10.55 or YTF03 protein. Once compounds are screened, those havingsuitable binding affinity to the BS10.55 or YTF03 protein can beevaluated in suitable biological assays, as are well known in the art,to determine whether they act as agonists or antagonists to a substrate.The availability of recombinant BS10.55 or YTF03 polypeptides alsoprovide well defined standards for calibrating such assays.

[0163] A preferred kit for determining the concentration of, forexample, a BS10.55 or YTF03 protein in a sample would typically comprisea labeled compound, e.g., antibody, having known binding affinity forthe BS10.55 or YTF03 protein, a source of BS10.55 or YTF03 protein(naturally occurring or recombinant), and a means for separating thebound from free labeled compound, for example, a solid phase forimmobilizing the BS10.55 or YTF03 protein. Compartments containingreagents, and instructions, will normally be provided.

[0164] Antibodies, including antigen binding fragments, specific for theBS10.55 or YTF03 protein, or fragments thereof, are useful in diagnosticapplications to detect the presence of elevated levels of BS10.55 orYTF03 protein and/or its fragments. Such diagnostic assays can employlysates, live cells, fixed cells, immunofluorescence, cell cultures,body fluids, and further can involve the detection of antigens relatedto the ligand in serum, or the like. Diagnostic assays may behomogeneous (without a separation step between free reagent and BS10.55or YTF03 protein complex) or heterogeneous (with a separation step).Various commercial assays exist, such as radioimmunoassay (RIA),enzyme-linked immunosorbentassay (ELISA), enzyme immunoassay (EIA),enzyme-multiplied immunoassay technique (EMIT), substrate-labeledfluorescent immunoassay (SLFIA), and the like. For example, unlabeledantibodies can be employed by using a second antibody which is labeledand which recognizes the antibody to a BS10.55 or YTF03 protein or to aparticular fragment thereof. Similar assays have also been extensivelydiscussed in the literature. See, e.g., Harlow and Lane (1988)Antibodies: A Laboratory Manual, CSH Press, NY; Chan (ed.) (1987)Immunoassay: A Practical Guide Academic Press, Orlando, Fla.; Price andNewman (eds.) (1991) Principles and Practice of Immunoassay StocktonPress, NY; and Ngo (ed.) (1988) Nonisotopic Immunoassay Plenum Press,NY.

[0165] Anti-idiotypic antibodies may have similar use to diagnosepresence of antibodies against a BS10.55 or YTF03 protein, as such maybe diagnostic of various abnormal states. For example, overproduction ofBS10.55 or YTF03 protein may result in production of variousimmunological or other medical reactions which may be diagnostic ofabnormal physiological states, e.g., in cell growth, acitivation, ordifferentiation.

[0166] Frequently, the reagents for diagnostic assays are supplied inkits, so as to optimize the sensitivity of the assay. For the subjectinvention, depending upon the nature of the assay, the protocol, and thelabel, either labeled or unlabeled antibody, or labeled BS10.55 or YTF03protein is provided. This is usually in conjunction with otheradditives, such as buffers, stabilizers, materials necessary for signalproduction such as substrates for enzymes, and the like. Preferably, thekit will also contain instructions for proper use and disposal of thecontents after use. Typically the kit has compartments for each usefulreagent. Desirably, the reagents are provided as a dry lyophilizedpowder, where the reagents may be reconstituted in an aqueous mediumproviding appropriate concentrations of reagents for performing theassay.

[0167] Many of the aforementioned constituents of the drug screening andthe diagnostic assays may be used without modification, or may bemodified in a variety of ways. For example, labeling may be achieved bycovalently or non-covalently joining a moiety which directly orindirectly provides a detectable signal. In any of these assays, theprotein, test compound, BS10.55 or YTF03 protein, or antibodies theretocan be labeled either directly or indirectly. Possibilities for directlabeling include label groups: radiolabels such as ¹²⁵I, enzymes (U.S.Pat. No. 3,645,090) such as peroxidase and alkaline phosphatase, andfluorescent labels (U.S. Pat. No. 3,940,475) capable of monitoring thechange in fluorescence intensity, wavelength shift, or fluorescencepolarization. Possibilities for indirect labeling include biotinylationof one constituent followed by binding to avidin coupled to one of theabove label groups.

[0168] There are also numerous methods of separating the bound from thefree antigen, or alternatively the bound from the free test compound.The BS10.55 or YTF03 protein can be immobilized on various matricesfollowed by washing. Suitable matrices include plastic such as an ELISAplate, filters, and beads. Methods of immobilizing the BS10.55 or YTF03protein to a matrix include, without limitation, direct adhesion toplastic, use of a capture antibody, chemical coupling, andbiotin-avidin. The last step in this approach usually involves theprecipitation of enzyme/antibody or enzyme substrate complex by variousmethods including those utilizing, e.g., an organic solvent such aspolyethylene glycol or a salt such as ammonium sulfate. Other suitableseparation techniques include, without limitation, the fluoresceinantibody magnetizable particle method described in Rattle, et al. (1984)Clin. Chem. 30:1457-1461, and the double antibody magnetic particleseparation as described in U.S. Pat. No. 4,659,678.

[0169] Methods for linking proteins or their fragments to the variouslabels have been extensively reported in the literature and do notrequire detailed discussion here. Many of the techniques involve the useof activated carboxyl groups either through the use of carbodiimide oractive esters to form peptide bonds, the formation of thioethers byreaction of a mercapto group with an activated halogen such aschloroacetyl, or an activated olefin such as maleimide, for linkage, orthe like. Fusion proteins will also find use in these applications.

[0170] Another diagnostic aspect of this invention involves use ofoligonucleotide or polynucleotide sequences taken from the sequence of aBS10.55 or YTF03 protein. These sequences can be used as probes fordetecting levels of the BS10.55 or YTF03 protein message in samples fromnatural sources, or patients suspected of having an abnormal condition,e.g., immune problem. The preparation of both RNA and DNA nucleotidesequences, the labeling of the sequences, and the preferred size of thesequences has received ample description and discussion in theliterature. Normally an oligonucleotide probe should have at least about14 nucleotides, usually at least about 18 nucleotides, and thepolynucleotide probes may be up to several kilobases. Various detectablelabels may be employed, most commonly radionuclides, particularly ³²P.However, other techniques may also be employed, such as using biotinmodified nucleotides for introduction into a polynucleotide. The biotinthen serves as the site for binding to avidin or antibodies, which maybe labeled with a wide variety of labels, such as radionuclides,fluorophores, enzymes, or the like. Alternatively, antibodies may beemployed which can recognize specific duplexes, including DNA duplexes,RNA duplexes, DNA-RNA hybrid duplexes, or DNA-protein duplexes. Theantibodies in turn may be labeled and the assay carried out where theduplex is bound to a surface, so that upon the formation of duplex onthe surface, the presence of antibody bound to the duplex can bedetected. The use of probes to the novel anti-sense RNA may be carriedout using many conventional techniques such as nucleic acidhybridization, plus and minus screening, recombinational probing, hybridreleased translation (HRT), and hybrid arrested translation (HART). Thisalso includes amplification techniques such as polymerase chain reaction(PCR).

[0171] Diagnostic kits which also test for the qualitative orquantitative presence of other markers are also contemplated. Diagnosisor prognosis may depend on the combination of multiple indications usedas markers. Thus, kits may test for combinations of markers. See, e.g.,Viallet, et al. (1989) Progress in Growth Factor Res. 1:89-97.

[0172] XII. Substrate Identification

[0173] Having isolated a protease or oxidoreductase, methods exist foridentifying a target substrate. For example, a candidate substrate canbe contacted with a BS10.55 or YTF03 protein in an enzymatic reaction.The resulting cleavage or oxidoreduction product can be analyzed, e.g.,using SDS-PAGE, HPLC, spectroscopy or other forms of analysis. Forexample, the molecular weight of a protease cleavage product should becompared against the molecular weights of the uncleaved substrate andthe BS10.55 protein. The successful candidate substrate will exhibit ashift to a lower molecular weight. Analysis of the substrate shoulddetermine what site specificity may exist for the enzyme under thetested conditions. Alternatively, if the protease acts by transformingan inactive substrate to the active form, the resulting activity can beassayed, e.g., by the result of the activated factor, e.g.,proliferation, apoptosis, or activation of a target cell.

[0174] Sequence specificity of products may allow search throughsequence databases to identify candidate proteins as physiologicallynatural substrates. Alternatively, the protease may be involve inantigen processing and presentation to appropriate immune cells.

[0175] Correspondingly, various candidate oxidation or reductionsubstrates may be evaluated. A spectroscopic or other method mayindicate what the enzyme has specificity for acting on.

[0176] The broad scope of this invention is best understood withreference to the following examples, which are not intended to limit theinvention to specific embodiments.

EXAMPLES

[0177] I. General Methods

[0178] Many of the standard methods below are described or referenced,e.g., in Maniatis, et al. (1982) Molecular Cloning, A Laboratory ManualCold Spring Harbor Laboratory, Cold Spring Harbor Press, NY; Sambrook,et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed.) Vols. 1-3,CSH Press, NY; Ausubel, et al., Biology Greene Publishing Associates,Brooklyn, N.Y.; or Ausubel, et al. (1987 and Supplements) CurrentProtocols in Molecular Biology Wiley/Greene, N.Y.; Innis, et al. (eds.)(1990) PCR Protocols: A Guide to Methods and Applications AcademicPress, NY. Methods for protein purification include such methods asammonium sulfate precipitation, column chromatography, electrophoresis,centrifugation, crystallization, and others. See, e.g., Ausubel, et al.(1987 and periodic supplements); Deutscher (1990) “Guide to ProteinPurification,” Methods in Enzymology vol. 182, and other volumes in thisseries; and manufacturer's literature on use of protein purificationproducts, e.g., Pharmacia, Piscataway, N.J., or Bio-Rad, Richmond,Calif. Combination with recombinant techniques allow fusion toappropriate segments (epitope tags), e.g., to a FLAG sequence or anequivalent which can be fused, e.g., via a protein-removable sequence.See, e.g., Hochuli (1989) Chemische Industrie 12:69-70; Hochuli (1990)“Purification of Recombinant Proteins with Metal Chelate Absorbent” inSetlow (ed.) Genetic Engineering, Principle and Methods 12:87-98, PlenumPress, NY; and Crowe, et al. (1992) QIAexpress: The High LevelExpression & Protein Purification System QUIAGEN, Inc., Chatsworth,Calif.

[0179] Standard immunological techniques are described, e.g., in Coligan(1991) Current Protocols in Immunology Wiley/Greene, NY; and Methods inEnzymology volumes. 70, 73, 74, 84, 92, 93, 108, 116, 121, 132, 150,162, and 163. Assays for neural cell biological activities aredescribed, e.g., in Wouterlood (ed. 1995) Neuroscience Protocols modules10, Elsevier; Methods in Neurosciences Academic Press; and NeuromethodsHumana Press, Totowa, N.J. Methodology of developmental systems isdescribed, e.g., in Meisami (ed.) Handbook of Human Growth andDevelopmental Biology CRC Press; and Chrispeels (ed.) MolecularTechniaues and Approaches in Developmental Biology Interscience.

[0180] FACS analyses are described in Melamed, et al. (1990) FlowCytometry and Sorting Wiley-Liss, Inc., New York, N.Y.; Shapiro (1988)Practical Flow Cytometry Liss, New York, N.Y.; and Robinson, et al.(1993) Handbook of Flow Cytometry Methods Wiley-Liss, New York, N.Y.

[0181] II. Isolation of Human BS10.55 or YTF03 Protein

[0182] A clone encoding the human BS10.55 or YTF03 protein is isolatedfrom a natural source by many different possible methods. Given thesequences provided herein, PCR primers or hybridization probes areselected and/or constructed to isolate a nucleic acid, e.g., genomic DNAsegments or cDNA reverse transcripts. Appropriate cell sources includehuman tissues, e.g., brain libraries. Tissue distribution below alsosuggests source tissues. Genetic and polymorphic or allelic variants areisolated by screening a population of individuals.

[0183] The BS10.55 gene was originally isolated from human germinalcenter dendritic cells (Grouard, et al. (1996) Nature 384:364-367)stimulated by overnight incubation with the anti-CD40 monoclonalantibody G28-5 (provided by E. A. Clark and J. F. Cantaloube). The PCRfragments were cloned via T-overhang into pCR11 (Invitrogen).

[0184] cDNA was prepared from 3×10⁶ germinal center dendritic cellspurified from human tonsils to 99% homogeneity and CD40 activated. ThecDNA was cut by the RsaI restriction enzyme and subtracted against cDNAfrom the cell line U937. U937 (ATCC CRL-1593) is a human is histiocyticlymphoma expressing many monocyte-like characteristics. The subtractionprocedure described recently by Diatchenko, et al. (1996) Proc. Natl.Acad. Sci. USA 93:6025-6030, was used with an adaptation to low cellnumber. The clone BS10.55 was discovered by random sequencing of thesubtracted germinal center dendritic cell library. The cDNA was extendedby RACE (rapid amplification of cohesive ends) using cDNA from in vitrogenerated dendritic cells. Caux, et al. (1992) Nature 360:258-261.

[0185] The YTF03 gene was found in a cDNA library made from a populationof 90% CD1a+ dendritic cells, proliferated in TNF-α and GM-CSF.

[0186] PCR based detection is performed by standard methods, preferablyusing appropriate primers from opposite ends of the coding sequence, butflanking segments might be selected for specific purposes.

[0187] Alternatively, hybridization probes are selected. Particular ATor GC contents of probes are selected depending upon the expectedhomology and mismatching expected. Appropriate stringency conditions areselected to balance an appropriate positive signal to background ratio.Successive washing steps are used to identify clones of greaterhomology.

[0188] Further clones will be isolated, e.g., using an antibody basedselection procedure. Standard expression cloning methods are appliedincluding, e.g., FACS staining of membrane associated expressionproduct. The antibodies are used to identify clones producing arecognized protein. Alternatively, antibodies are used to purify aBS10.55 or YTF03 protein, with protein sequencing and standard means toisolate a gene encoding that protein.

[0189] Genomic or cDNA sequence based methods will also allow foridentification of sequences naturally available, or otherwise, whichexhibit homology to the provided sequences.

[0190] III. Isolation of Mouse BS10.55 or YTF03 Protein

[0191] Similar methods are used as above to isolate an appropriateBS10.55 or YTF03 protein gene. Similar source materials as indicatedabove are used to isolate natural genes, including genetic, polymorphic,allelic, or strain variants. Species variants are also isolated usingsimilar methods. Various sequence databases may suggest related orcounterpart sequences. See, e.g., Capone, et al. (1996) J. Immunol.157:969-973.

[0192] IV. Isolation of an Avian BS10.55 or YTF03 Protein Clone

[0193] An appropriate avian source is selected as above. Similar methodsare utilized to isolate other species variants, though the level ofsimilarity will typically be lower for avian BS10.55 or YTF03 protein ascompared to a human to mouse sequence.

[0194] V. Expression; Purification; Characterization

[0195] With an appropriate clone from above, the coding sequence isinserted into an appropriate expression vector. This may be in a vectorspecifically selected for a prokaryote, yeast, insect, or highervertebrate, e.g., mammalian expression system. Standard methods areapplied to produce the gene product, preferably as a soluble secretedmolecule, but will, in certain instances, also be made as anintracellular protein. Intracellular proteins typically require celllysis to recover the protein, and insoluble inclusion bodies are acommon starting material for further purificiation.

[0196] With a clone encoding a vertebrate BS10.55 or YTF03 protein,recombinant production means are used, although natural forms may bepurified from appropriate sources, e.g., expressing cell lines. Theprotein product is purified by standard methods of protein purification,in certain cases, e.g., coupled with immunoaffinity methodsImmunoaffinity methods are used either as a purification step, asdescribed above, or as a detection assay to determine the partitionproperties of the protein.

[0197] Preferably, the protein is secreted into the medium, and thesoluble product is purified from the medium in a soluble form. Standardpurification techniques applied to soluble protiens are then applied,with enzyme assays or immunodetection methods useful for following wherethe protease purifies. Alternatively, as described above, inclusionbodies from prokaryotic expression systems are a useful source ofmaterial. Typically, the insoluble protein is solubilized from theinclusion bodies and refolded using standard methods. Purificationmethods are developed as described above.

[0198] In certain embodiments, the protein is made in a eukaryotic cellwhich glycosylates the protein normally. The purification methods may beaffected thereby, as may biological activities. The intact protein canbe processed to release the protein domain, probably due to a cleavageevent. While recombinant protein appears to be processed, thephysiological processes which normally do such in native cells remain tobe determined.

[0199] The product of the purification method described above ischaracterized to determine many structural features. Standard physicalmethods are applied, e.g., amino acid analysis and protein sequencing.The resulting protein is subjected to CD spectroscopy and otherspectroscopic methods, e.g., NMR, ESR, mass spectroscopy, etc. Theproduct is characterized to determine its molecular form and size, e.g.,using gel chromatography and similar techniques. Understanding of thechromatographic properties will lead to more gentle or efficientpurification methods.

[0200] Prediction of glycosylation sites may be made, e.g., as reportedin Hansen, et al. (1995) Biochem. J. 308:801-813. Standard methods forassaying oxidoreductases, particularly monoamine oxidases, are found,e.g., in Methods in Enzymology; Moser, et al. (1995) J. Bioenerg.27:263-274; Lawen, et al. (1994) Mol. Aspects Med. 15:supp:13-27; andKoishi, et al. (1997) J. Biol. Chem. 272:₂₅₇₀-2577.

[0201] VI. Preparation of Antibodies Against Vertebrate BS10.55 or YTF03Protein

[0202] With protein produced and purified, as above, animals areimmunized to produce antibodies. Polyclonal antiserum may be raisedusing non-purified antigen, though the resulting serum will exhibithigher background levels. Preferably, the antigen is purified usingstandard protein purification techniques, including, e.g., affinitychromatography using polyclonal serum indicated above. Presence ofspecific antibodies is detected using defined synthetic peptidefragments.

[0203] Alternatively, polyclonal serum is raised against a purifiedantigen, purified as indicated above, or using synthetic peptides. Aseries of overlapping synthetic peptides which encompass all of the fulllength sequence, if presented to an animal, will produce serumrecognizing most linear epitopes on the protein. Such an antiserum isused to affinity purify protein. This purified protein, in turn, may beused to immunize another animal to produce another antiserumpreparation.

[0204] Standard techniques are used to generate induce monoclonalantibodies to either unpurified antigen, or, preferably, purifiedantigen.

[0205] VII. Cellular and Tissue Distribution

[0206] Distribution of the protein or gene products are determined,e.g., using immunohistochemistry with an antibody reagent, as producedabove, or by screening for nucleic acids encoding the BS10.55 or YTF03protein. Either hybridization or PCR methods are used to detect DNA,cDNA, or message content. Histochemistry allows determination of thespecific cell types within a tissue which express higher or lower levelsof message or DNA. Antibody techniques are useful to quantitate proteinin a biological sample, including a liquid or tissue sample.Immunoassays are developed to quantitate protein.

[0207] Hybridization techniques were applied to the tissue types indescribed above with positive or negative results, as indicated. Thecommercial tissue blots may have more significant cellular contaminationfrom other cells, e.g., from blood or other cells which are in thetissue.

[0208] By PCR the BS10.55 sequence is expressed in germinal centerdendritic cells and in vitro generated dendritic cells, eitherstimulated or non-stimulated (Caux, et al. (1992) Nature 360:258-261). Afaint signal may have been detected in CHA kidney epithelial carcinomacell line. No detectable signal was observed in the hematopoieticprecursor line TF1, Jurkat T cell line, MRC5 lung fibroblast sarcomacell line, JY B cell line, or U937 pre-monocytic cell line.

[0209] By Northern blot analyses a 2.9 kb message was detected in RNAfrom adult small intestine, but not in similar abundance in any of adultPBL, colon, ovary, testis, prostate, thymus, spleen, pancreas, kidney,skeletal muscle, liver, lung, placenta, brain, or heart. No signal wasdetected in resting DC, activated DC, monocytes, granulocytes, restingPBL, activated PBL, or B cells.

[0210] By PCR analysis, expression of YTF03 is strongest in monocyte M6(elutriated monocytes activated with LPS 6 h), 70% DC (resting 70% CD1a+dendritic cells, proliferated in TNF-α and GM-CSF), Dl (dendritic cellsstimulated 1 h in PMA and ionomycin), D6 (dendritic cells stimulated 6 hin PMA and ionomycin), HY06R (resting Th1 clone), and HY06α (activatedwith anti-peptide, anergic clone). Expression is almost as strong inMonocyte C+ (elutriated monocytes activated with LPS, IFN-γ, and IL-10),D5 DC (resting dendritic cells cultured 5 d in GM-CSF and IL-4), DC mix(dendritic cells stimulated with a mixture of cytokines), and HY06A(activated with anti-CD28 and anti-CD3).

[0211] Expression of YTF03 is not as strong in C- (elutriated monocyteactivated with LPS, IFN-γ, and anti-IL-10), M1 (elutriated monocytesactivated with LPS 1 h) PBMCA (activated using T cell stimulationconditions, with anti-CD3 and PMA), HY935A (activated with anti-CD28 andanti-CD3), BC (pool of EBV transformed lines), SplenoA (splenocytesactivated using B cell stimulating conditions, with anti-CD40 and IL-4),NKR (resting NK cell pool), NKA (NK cell pool activated 6 h with PMA andionomycin; NKA is slightly stonger than NKR), and spleen. Signal is muchweaker in U937 (pre-monocytic cell line), brain, small intestine, andvery faint in HY935R (resting Th2 clone), adipose, and placenta. It isquestionable whether YTF03 is expressed in kidney. No expression wasdetected in: PBMCR (resting PBMC), SplenoR (resting splenocytes), lung,liver, heart, gall bladder, ovary, testes, uterus, and RAW. In summary,YTF03 is expressed mainly in DC and monocytes, and to a lesser extent insome T cells.

[0212] VIII. Structure Activity Relationship

[0213] Information on the criticality of particular residues isdetermined using standard procedures and analysis. Standard mutagenesisanalysis is performed, e.g., by generating many different variants atdetermined positions, e.g., at the positions identified above, andevaluating biological activities of the variants. This may be performedto the extent of determining positions which modify activity, or tofocus on specific positions to determine the residues which can besubstituted to either retain, block, or modulate biological activity.

[0214] Alternatively, analysis of natural variants can indicate whatpositions tolerate natural mutations. This may result from populationalanalysis of variation among individuals, or across strains or species.Samples from selected individuals are analysed, e.g., by PCR analysisand sequencing. This allows evaluation of population polymorphisms.

[0215] IX. Additional Genes

[0216] One additional gene has been characterized and described. SeeTable 3. Nucleic acids may be used, as described above, to express andassay biological samples for hybridizing or related nucleic acids. Theymay also be used to express recombinant protein, which can be enrichedor purified for the expression products. Those products can be used tofurther characterize biochemically and physiologically the protein.Antibodies may be made, both for diagnostic purposes, and to modulatebiological activity of the protein itself. Such reagents may also havetherapeutic applications, and can be used as described above. Proteinand nucleic acid variants will be useful as described above. TABLE 3APD08 gene from a human, characteristic of primate embodiments. Thenucleotide and predicted amino acid sequence. SEQ ID NO: 5 and 6. Thecoding sequence runs from about 69 to 1928. The encoded protein containstwo domains which each exhibit homology to a GTPase. The amino terminalGTPase domain is similar to the Rho family members, most of which aresmaller proteins. The cDNA appears to be widely expressed, but sequenceshould be characteristic of genetic origin, and may be useful, e.g., indifferentiating genetic origin, or genetic relation. Thus, the sequencemay be useful in identifying human tissues. Related gene sequences bycomparison search using standard algorithms include, e.g., thoseidentified by GenBank numbers H07061, H13318, N52992, H96929, H07062,R40014, and R13644. GGGTCGACCA CGCGTCCGAC CAGGTCGGGG CCGGGTTCCGGGTCGGGGAG CGGCTCCGGG 60 CGGCAGCT ATG AGG CGG GAC GTG CGC ATC CTG TTACTG GGC GAG GCC CAG 110          Met Arg Arg Asp Val Arg Ile Leu Leu LeuGly Glu Ala Gln            1               5              10 GTG GGG AAGACG TCG CTG ATC CTG TCC CTG GTG GGC GAG GAG TTC CCC 158 Val Gly Lys ThrSer Leu Ile Leu Ser Leu Val Gly Glu Glu Phe Pro 15                  20                  25                  30 GAG GAGGTC CCT CCC CGC GCG GAG GAG ATC ACG ATC CCC GCG GAC GTC 206 Glu Glu ValPro Pro Arg Ala Glu Glu Ile Thr Ile Pro Ala Asp Val                 35                  40                  45 ACC CCG GAGAAG GTG CCC ACC CAC ATC GTG GAC TAC TCA GAA GCC GAG 254 Thr Pro Glu LysVal Pro Thr His Ile Val Asp Tyr Ser Glu Ala Glu             50                  55                  60 CAG ACG GAC GAGGAG CTG CGG GAG GAG ATC CAC AAG GCA AAC GTG GTG 302 Gln Thr Asp Glu GluLeu Arg Glu Glu Ile His Lys Ala Asn Val Val         65                  70                  75 TGT GTG GTG TAT GACGTC TCT GAG GAG GCC ACC ATT GAG AAG ATT CGA 350 Cys Val Val Tyr Asp ValSer Glu Glu Ala Thr Ile Glu Lys Ile Arg     80                  85                  90 ACT AAG TGG ATC CCA CTGGTG AAT GGG GGG ACC ACG CAG GGG CCC AGG 398 Thr Lys Trp Ile Pro Leu ValAsn Gly Gly Thr Thr Gln Gly Pro Arg 95                 100                 105                 110 GTG CCCATC ATC CTA GTG GGC AAC AAG TCA GAC CTG CGG TCG GGG AGC 446 Val Pro IleIle Leu Val Gly Asn Lys Ser Asp Leu Arg Ser Gly Ser                115                 120                 125 TCC ATG GAGGCC GTG CTC CCC ATC ATG AGC CAG TTT CCC GAG ATT GAG 494 Ser Met Glu AlaVal Leu Pro Ile Met Ser Gln Phe Pro Glu Ile Glu            130                 135                 140 ACC TGC GTG GAGTGT TCG GCC AAG AAC CTG AGG AAC ATC TCA GAG CTG 542 Thr Cys Val Glu CysSer Ala Lys Asn Leu Arg Asn Ile Ser Glu Leu        145                 150                 155 TTC TAC TAC GCC CAGAAG GCC GTC CTG CAT CCC ACA GCC CCC CTC TAT 590 Phe Tyr Tyr Ala Gln LysAla Val Leu His Pro Thr Ala Pro Leu Tyr    160                 165                 170 GAC CCT GAG GCC AAG CAGTTG AGG CCC GCG TGC GCC CAG GCG CTG ACG 638 Asp Pro Glu Ala Lys Gln LeuArg Pro Ala Cys Ala Gln Ala Leu Thr175                 180                 185                 190 CGC ATCTTC AGG CTC TCA GAT CAG GAC CTG GAC CAG GCG CTC AGT GAC 686 Arg Ile PheArg Leu Ser Asp Gln Asp Leu Asp Gln Ala Leu Ser Asp                195                 200                 205 GAA GAG CTCAAC GCT TTC CAG CAG AAA TCC TGC TTT GGG CAC CCC CTG 734 Glu Glu Leu AsnAla Phe Gln Gln Lys Ser Cys Phe Gly His Pro Leu            210                 215                 220 GCC CCG CAG GCCCTG GAG GAC GTG AAG ACG GTG GTG TGC AGG AAC GTG 782 Ala Pro Gln Ala LeuGlu Asp Val Lys Thr Val Val Cys Arg Asn Val        225                 230                 235 GCG GGC GGC GTG CGGGAG GAC CGG CTG ACC CTG GAT GGT TTC CTC TTC 830 Ala Gly Gly Val Arg GluAsp Arg Leu Thr Leu Asp Gly Phe Leu Phe    240                 245                 250 CTG AAC ACG CTC TTC ATCCAG CGC GGC CGG CAC GAG ACC ACC TGG ACC 878 Leu Asn Thr Leu Phe Ile GlnArg Gly Arg His Glu Thr Thr Trp Thr255                 260                 265                 270 ATC CTGCGG CGC TTC GGC TAC AGC GAT GCC CTG GAG CTG ACT GCG GAC 926 Ile Leu ArgArg Phe Gly Tyr Ser Asp Ala Leu Glu Leu Thr Ala Asp                275                 280                 285 TAT CTC TCCCCT CTG ATC CAC GTG CCC CCC GGC TGC AGC ACG GAG CTC 974 Tyr Leu Ser ProLeu Ile His Val Pro Pro Gly Cys Ser Thr Glu Leu            290                 295                 300 AAC CAC CTT GGCTAC CAG TTT GTG CAG AGA GTG TTT GAG AAG CAC GAC 1022 Asn His Leu Gly TyrGln Phe Val Gln Arg Val Phe Glu Lys His Asp        305                 310                 315 CAG GAC CGC GAC GGCGCC CTC TCG CCC GTG GAG CTG CAA AGC CTT TTC 1070 Gln Asp Arg Asp Gly AlaLeu Ser Pro Val Glu Leu Gln Ser Leu Phe    320                 325                 330 AGT GTG TTC CCA GCA GCGCCC TGG GGC CCC GAG CTC CCA CGC ACA GTC 1118 Ser Val Phe Pro Ala Ala ProTrp Gly Pro Glu Leu Pro Arg Thr Val335                 340                 345                 350 CGC ACAGAG GCC GGC CGG TTG CCC CTG CAC GGA TAC CTC TGC CAG TGG 1166 Arg Thr GluAla Gly Arg Leu Pro Leu His Gly Thr Leu Cys Gln Trp                355                 360                 365 ACC CTG GTGACC TAC CTG GAC GTC CGG AGC TGC CTT GGA CAC CTA GGC 1214 Thr Leu Val ThrTyr Leu Asp Val Arg Ser Cys Leu Gly His Leu Gly            370                 375                 380 TAC CTG GGC TACCCC ACC CTC TGT GAG CAG GAC CAG GCC CAT GCC ATC 1262 Tyr Leu Gly Tyr ProThr Leu Cys Glu Gln Asp Gln Ala His Ala Ile        385                 390                 395 ACA GTC ACT CGT GAGAAG AGG CTG GAC CAG GAG AAG GGA CAG ACG CAG 1310 Thr Val Thr Arg Glu LysArg Leu Asp Gln Glu Lys Gly Gln Thr Gln    400                 405                 410 TGG AGC GTC CTC CTG TGCAAG GTG GTA GGG GCC CGT GGA GTG GGC AAG 1358 Trp Ser Val Leu Leu Cys LysVal Val Gly Ala Arg Gly Val Gly Lys415                 420                 425                 430 TCT GCCTTC CTG CAG GCC TTT CTC GGC CGC GGC CTG GGG CAC CAG GAC 1406 Ser Ala PheLeu Gln Ala Phe Leu Gly Arg Gly Leu Gly His Gln Asp                435                 440                 445 ACG AGG GAGCAG CCT CCC GGC TAC GCC ATC GAC ACG GTG CAG GTC AAT 1454 Thr Arg Glu GlnPro Pro Gly Tyr Ala Ile Asp Thr Val Gln Val Asn            450                 455                 460 GGA CAG GAG AAGTAC TTG ATC CTC TGT GAG GTG GGC ACA GAT GGT CTG 1502 Gly Gln Glu Lys TyrLeu Ile Leu Cys Glu Val Gly Thr Asp Gly Leu        465                 470                 475 CTG GCC ACA TCG CTGGAC GCC ACC TGT GAC GTT GCC TGC TTG ATG TTT 1550 Leu Ala Thr Ser Leu AspAla Thr Cys Asp Val Ala Cys Leu Met Phe    480                 485                 490 GAT GGC AGT GAC CCA AAGTCC TTT GCA CAT TGT GCC AGC GTC TAC AAG 1598 Asp Gly Ser Asp Pro Lys SerPhe Ala His Cys Ala Ser Val Tyr Lys495                 500                 505                 510 CAC CATTAC ATG GAC GGG CAG ACC CCC TGC CTC TTT GTC TCC TCC AAG 1646 His His TyrMet Asp Gly Gln Thr Pro Cys Leu Phe Val Ser Ser Lys                515                 520                 525 GCC GAC CTGCCC GAA GGT GTC GCG GTG TCT GGC CCA TCA CCG GCC GAG 1694 Ala Asp Leu ProGlu Gly Val Ala Val Ser Gly Pro Ser Pro Ala Glu            530                 535                 540 TTT TGC CGC AAGCAC CGG CTA CCC GCT CCC GTG CCG TTC TCC TGT GCT 1742 Phe Cys Arg Lys HisArg Leu Pro Ala Pro Val Pro Phe Ser Cys Ala        545                 550                 555 GGC CCA GCC GAG CCCAGC ACC ACC ATC TTC ACC CAG CTC GCC ACC ATG 1790 Gly Pro Ala Glu Pro SerThr Thr Ile Phe Thr Gln Leu Ala Thr Met    560                 565                 570 GCC GCC TTC CCA CAT TTGGTC CAC GCA GAG CTG CAT CCC TCT TCC TTC 1838 Ala Ala Phe Pro His Leu ValHis Ala Glu Leu His Pro Ser Ser Phe575                 580                 585                 590 TGG CTCCGG GGG CTG CTG GGG GTT GTC GGG GCC GCC GTG GCC GCA GTC 1886 Trp Leu ArgGly Leu Leu Gly Val Val Gly Ala Ala Val Ala Ala Val                595                 600                 605 CTC AGC TTCTCA CTC TAC AGG GTC CTG GTG AAG AGC CAG TGA 1928 Leu Ser Phe Ser Leu TyrArg Val Leu Val Lys Ser Gln  *            610                 615                 620 GGCCCCTGGTACCCAAGCCC CCTCCCCTGA CCTGGGTGTG CCTCGCTGCT GGGGCTCTGC 1988 ACTTTTTGTTTCTGAAGGCA GTCGATCTGC AGCGGGGCCT TATGCTGCCA TGCACTGCCC 2108 TGGCTCCTGCCGGACCCCCA GGGTGGGCCG TGGCAGGTGG CTGAGCAGGA GCTCCCAAGT 2168 GCCGGCCACCGCTGTCAGGG ATTGCCCACC CCTGGGCATC ATGTGTGTGG GGCCGGGGAG 2228 CACAGGTGTGGGAGCTGGTG ACCCCAGACC CAGAATTCTC AGGGCTCTAC CCCCCTTTCC 2288 TGGTCCTAGGTGGCCAGTGG GTATGAGGAG GGCTGGAAGG CAGAGCTTTG GGCCAAAAGC 2348 AGGCGTTGGGGGGTCCCCCC TCAAGTTTGG AGCCGTTTCC GTGGTTGTAG CAGAGGACCG 2408 GAGGTTGGGTTCCTGATTAA ACTTCACTGT GTGTTTTCTA TCTCGGATCC CAGTCTCTGA 2468 AGACAACTTGCTTTGATTCA ACCTAAAAAA AAAAAAAAAA AAAAAAAA 2516

[0217] The present invention provides a binding compound comprising anantibody binding site which specifically binds to primate APD08 protein;a nucleic acid comprising sequence encoding at least 12 amino acids ofprimate APD08 protein; a substantially pure protein which isspecifically recognized by the above antibody binding site; asubstantially pure primate APD08 protein or peptide thereof; and afusion protein comprising a 30 amino acid sequence portion of primateAPD08 protein sequence.

[0218] In certain binding compound embodiments, the antibody bindingsite is specifically immunoreactive with a protein of SEQ ID NO: 6; israised against a purified or recombinantly produced primate APD08protein; is immunoselected on a substantially purified or recombinantlyproduced primate APD08 protein; is in a monoclonal antibody, Fab, orF(ab)₂; is detectably labeled; is attached to a solid substrate; is froma rabbit or mouse; binds with a Kd of at least about 300 μM; is fused toanother protein segment; is in a chimeric antibody; or is couped toanother chemical moiety.

[0219] The invention also provides a method of making anantigen-antibody complex, comprising a step of contacting a primatebiological sample to a specific binding antibody described. In preferredembodiments, the method further includes steps to purify the antigen orantibody.

[0220] Alternative embodiments provide an antibody binding site whereinthe binding site is detected in a biological sample by a methodcomprising the steps of contacting a binding agent having an affinityfor APD08 protein with the biological sample; incubating the bindingagent with the biological sample to form a binding agent:APD08 proteincomplex; and detecting the complex. In certain embodiments, thebiological sample is human, and the binding agent is an antibody.

[0221] The invention also provides kits containing a compositiondescribed above and instructional material for the use of thecomposition; or segregation of the composition into a container.Typically, the kit is used to make a qualitative or quantitativeanalysis.

[0222] The invention also embraces a cell comprising an antibodydescribed above; a cell transfected with a nucleic acid described above;or a cell comprising a fusion protein described above.

[0223] In nucleic acid embodiments, the nucleic acid may encode apolypeptide which specifically binds an antibody generated against animmunogen selected from the group consisting of the mature polypeptideof SEQ ID NO: 6. Alternatively, the nucleic acid may encode at least 12amino acids of SEQ ID NO: 6; comprise sequence of at least about 39nucleotides selected from protein coding portions of SEQ ID NO: 5;hybridize to SEQ ID NO: 5 under stringent wash conditions of at least45° C. and less than about 150 mM salt; comprise sequence made by asynthetic method; be an expression vector; be detectably labeled; beattached to a solid substrate; be from human; bind with a Kd of at leastabout 300 μM; be fused to another nucleic acid segment; be coupled toanother chemical moiety; be operably associated with promoter, ribosomebinding site, or poly-A addition site; be a PCR product; be transformedinto a cell, including a bacterial cell; be in a sterile composition; becapable of selectively hybridizing to a nucleic acid encoding an APD08protein; comprise a natural sequence; comprise a mature protein codingsegment of SEQ ID NO: 5; encode a GTPase active portion of APD08; bedetected in a biological sample by a method comprising: contacting abiological sample with a nucleic acid probe capable of selectivelyhybridizing to said nucleic acid, incubating the nucleic acid probe withthe biological sample to form a hybrid of the nucleic acid probe withcomplementary nucleic acid sequences present in the biological sample;and determining the extent of hybridization of the nucleic acid probe tothe complementary nucleic acid sequences, including the method where thenucleic acid probe is capable of hybridizing to a nucleic acid encodinga mature polypeptide of SEQ ID NO 6.

[0224] In protein or polypeptide embodiments, the protein may bind witha Kd of at least about 300 μM to an antibody generated against animmunogen of the polypeptides of SEQ ID NO: 6; be immunoselected on anantibody which selectively binds a polypeptide of SEQ ID NO: 6; comprisesequence of at least 12 contiguous residues of SEQ ID NO: 6; exhibit apost-translational modification pattern distinct from natural APD08; be3-fold or fewer substituted from natural sequence; be recombinantlyproduced; be denatured; have sequence of full length naturalpolypeptide; be detectably labeled; be attached to a solid substrate; befrom human; be in a sterile composition; be fused to another proteinsegment; be coupled to another chemical moiety; comprise at least afragment of at least 32 amino acid residues from a human APD08 protein;comprise mature polypeptide sequence of SEQ ID NO 6; be a solubleprotein; be a naturally occurring protein; or be a GTPase active portionof APD08.

[0225] The invention also provides an isolated protein whichspecifically binds to an antibody generated against an immunogen whichis the full length polypeptide of SEQ ID NO: 6. Preferably such proteinbinds to the antibody with a Kd of at least about 300 μM; isimmunoselected on an antibody which selectively binds a polypeptide ofSEQ ID NO: 6; comprises sequence of at least 12 contiguous residues ofSEQ ID NO: 6; exhibits a post-translational modification patterndistinct from natural APD08; is 3-fold or fewer substituted from naturalsequence; is recombinantly produced; is denatured; has sequence of fulllength natural polypeptide; is detectably labeled; is attached to asolid substrate; is from human; is in a sterile composition; is fused toanother protein segment; is coupled to another chemical moiety;comprises at least a fragment of at least 32 amino acid residues from ahuman APD08 protein; comprises mature polypeptide sequence selected fromSEQ ID NO 6; is a soluble protein; or comprises a GTPase activity ofAPD08.

[0226] In certain other embodiments, the invention embraces a fusionprotein described above, which comprises sequence from an enzymaticallyactive portion of SEQ ID NO: 6. Preferably such protein binds with a Kdof at least about 300 μM to an antibody generated against an immunogenhaving sequence of a polypeptide of SEQ ID NO. 6; is immunoselected onan antibody which selectively binds a polypeptide of SEQ ID NO: 6;comprises sequence of at least 12 contiguous residues of SEQ ID NO: 6;is recombinantly produced; is denatured; has sequence of full lengthnatural polypeptide; is detectably labeled; is attached to a solidsubstrate; comprises sequence from human; is in a sterile composition;is fused to another protein segment; is coupled to another chemicalmoiety; comprises at least a fragment of at least 32 amino acid residuesfrom a human APD08 protein; comprises mature polypeptide sequence fromSEQ ID NO: 6; is a soluble protein; or comprises a GTPase activity ofAPD08.

[0227] The invention also provides a substantially pure proteindescribed above which comprises a GTPase activity of APD08.

[0228] APD08 is tested for GTPase activity by methods well known in theart. Assays are described or referred to in, e.g., Dickey, et-al. (eds.1993) GTPases in Biology, vol. 108, parts I and II, Springer-Verlag, NewYork, N.Y.; Balch, et al. (eds. 1995) Meth. Enzymol. Vols. 255-257,Academic Press, San Diego, Calif.; Tapon, et al. (1997) Curr. Opin. CellBiol. 9:86-92; Hotchin, et al. (1996) Cancer Surv. 27:311-322; Symons(1996) Trends Biochem Sci. 21:178-181; Hilgenfeld (1995) Curr Opin.Struct. Biol. 5:810-817; Nuoffer, et al. (1994) Annu. Rev. Biochem,63:949-990; Spaargaren, et al. (1995) Gene Expr. 4:345-356; and Hall(1992) Mol. Cell. Biol. 3:475-479. Based upon this activity, the enzymewill be useful in screening for agonists and antagonists, and inmodulating related biochemistry or metabolism. Similar methods to thosedescribed above will be used to identify the cells and tissuespecificity of expression.

[0229] All references cited herein are incorporated herein by referenceto the same extent as if each individual publication or patentapplication was specifically and individually indicated to beincorporated by reference in its entirety for all purposes.

[0230] Many modifications and variations of this invention can be madewithout departing from its spirit and scope, as will be apparent tothose skilled in the art. The specific embodiments described herein areoffered by way of example only, and the invention is to be limited onlyby the terms of the appended claims, along with the full scope ofequivalents to which such claims are entitled.

1 6 2280 base pairs nucleic acid single linear cDNA CDS 61..1470 1CGCCCGGGCA GGTGAGAAAT TGGAGAAGAT AAAACTGGAC ACTGGGGAGA CCACAACTTC 60 ATGCTG CGT GGG ATC TCC CAG CTA CCT GCA GTG GCC ACC ATG TCT TGG 108 Met LeuArg Gly Ile Ser Gln Leu Pro Ala Val Ala Thr Met Ser Trp 1 5 10 15 GTCCTG CTG CCT GTA CTT TGG CTC ATT GTT CAA ACT CAA GCA ATA GCC 156 Val LeuLeu Pro Val Leu Trp Leu Ile Val Gln Thr Gln Ala Ile Ala 20 25 30 ATA AAGCAA ACA CCT GAA TTA ACG CTC CAT GAA ATA GTT TGT CCT AAA 204 Ile Lys GlnThr Pro Glu Leu Thr Leu His Glu Ile Val Cys Pro Lys 35 40 45 AAA CTT CACATT TTA CAC AAA AGA GAG ATC AAG AAC AAC CAG ACA GAA 252 Lys Leu His IleLeu His Lys Arg Glu Ile Lys Asn Asn Gln Thr Glu 50 55 60 AAG CAT GGC AAAGAG GAA AGG TAT GAA CCT GAA GTT CAA TAT CAG ATG 300 Lys His Gly Lys GluGlu Arg Tyr Glu Pro Glu Val Gln Tyr Gln Met 65 70 75 80 ATC TTA AAT GGAGAA GAA ATC ATT CTC TCC CTA CAA AAA ACC AAG CAC 348 Ile Leu Asn Gly GluGlu Ile Ile Leu Ser Leu Gln Lys Thr Lys His 85 90 95 CTC CTG GGG CCA GACTAC ACT GAA ACA TTG TAC TCA CCC AGA GGA GAG 396 Leu Leu Gly Pro Asp TyrThr Glu Thr Leu Tyr Ser Pro Arg Gly Glu 100 105 110 GAA ATT ACC ACG AAACCT GAG AAC ATG GAA CAC TGT TAC TAT AAA GGA 444 Glu Ile Thr Thr Lys ProGlu Asn Met Glu His Cys Tyr Tyr Lys Gly 115 120 125 AAC ATC CTA AAT GAAAAG AAT TCT GTT GCC AGC ATC AGT ACT TGT GAC 492 Asn Ile Leu Asn Glu LysAsn Ser Val Ala Ser Ile Ser Thr Cys Asp 130 135 140 GGG TTG AGA GGA TACTTC ACA CAT CAT CAC CAA AGA TAC CAG ATA AAA 540 Gly Leu Arg Gly Tyr PheThr His His His Gln Arg Tyr Gln Ile Lys 145 150 155 160 CCT CTG AAA AGCACA GAC GAG AAA GAA CAT GCC GTC TTT ACA TCT AAC 588 Pro Leu Lys Ser ThrAsp Glu Lys Glu His Ala Val Phe Thr Ser Asn 165 170 175 CAG GAG GAA CAAGAC CCA GCT AAC CAC ACA TGT GGT GTG AAG AGC ACT 636 Gln Glu Glu Gln AspPro Ala Asn His Thr Cys Gly Val Lys Ser Thr 180 185 190 GAC GGG AAA CAAGGC CCA ATT CGA ATC TCT AGA TCA CTC AAA AGC CCA 684 Asp Gly Lys Gln GlyPro Ile Arg Ile Ser Arg Ser Leu Lys Ser Pro 195 200 205 GAG AAA GAA GACTTT CTT CGG GCA CAG AAA TAC ATT GAT CTC TAT TTG 732 Glu Lys Glu Asp PheLeu Arg Ala Gln Lys Tyr Ile Asp Leu Tyr Leu 210 215 220 GTG CTG GAT AATGCC TTT TAT AAG AAC TAT AAT GAG AAT CTA ACT CTG 780 Val Leu Asp Asn AlaPhe Tyr Lys Asn Tyr Asn Glu Asn Leu Thr Leu 225 230 235 240 ATA AGA AGCTTT GTG TTT GAT GTG ATG AAC CTA CTC AAT GTG ATA TAT 828 Ile Arg Ser PheVal Phe Asp Val Met Asn Leu Leu Asn Val Ile Tyr 245 250 255 AAC ACC ATAGAT GTT CAA GTG GCC TTG GTA GGT ATG GAA ATC TGG TCT 876 Asn Thr Ile AspVal Gln Val Ala Leu Val Gly Met Glu Ile Trp Ser 260 265 270 GAT GGG GATAAG ATA AAG GTG GTG CCC AGC GCA AGC ACC ACG TTT GAC 924 Asp Gly Asp LysIle Lys Val Val Pro Ser Ala Ser Thr Thr Phe Asp 275 280 285 AAC TTC CTGAGA TGG CAC AGT TCT AAC CCG GGG AAA AAG ATC CAC GAC 972 Asn Phe Leu ArgTrp His Ser Ser Asn Pro Gly Lys Lys Ile His Asp 290 295 300 CAT GCT CAGCTT CTC AGC GGG ATT AGC TTC AAC AAT CGA CGT GTG GGA 1020 His Ala Gln LeuLeu Ser Gly Ile Ser Phe Asn Asn Arg Arg Val Gly 305 310 315 320 CTG GCAGCT TCA AAT TCC TTG TGT TCC CCA TCT TCG GTT GCT GTT ATT 1068 Leu Ala AlaSer Asn Ser Leu Cys Ser Pro Ser Ser Val Ala Val Ile 325 330 335 GAG GCTAAA AAA AAG AAT AAT GTG GCT CTT GTA GGA GTG ATG TCA CAT 1116 Glu Ala LysLys Lys Asn Asn Val Ala Leu Val Gly Val Met Ser His 340 345 350 GAG CTGGGC CAT GTC CTT GGT ATG CCT GAT GTT CCA TTC AAC ACC AAG 1164 Glu Leu GlyHis Val Leu Gly Met Pro Asp Val Pro Phe Asn Thr Lys 355 360 365 TGT CCCTCT GGC AGT TGT GTG ATG AAT CAG TAT CTG AGT TCA AAA TTC 1212 Cys Pro SerGly Ser Cys Val Met Asn Gln Tyr Leu Ser Ser Lys Phe 370 375 380 CCA AAGGAT TTC AGT ACA TCT TGC CGT GCA CAT TTT GAA AGA TAC CTT 1260 Pro Lys AspPhe Ser Thr Ser Cys Arg Ala His Phe Glu Arg Tyr Leu 385 390 395 400 TTATCT CAG AAA CCA AAG TGC CTG CTG CAA GCA CCT ATT CCT ACA AAT 1308 Leu SerGln Lys Pro Lys Cys Leu Leu Gln Ala Pro Ile Pro Thr Asn 405 410 415 ATAATG ACA ACA CCA GTG TGT GGG AAC CAC CTT CTA GAA GTG GGA GAA 1356 Ile MetThr Thr Pro Val Cys Gly Asn His Leu Leu Glu Val Gly Glu 420 425 430 GACTGT GAT TGT GGC TCT CCT AAG GAG TGT ACC AGT CTC TGC TGT GAA 1404 Asp CysAsp Cys Gly Ser Pro Lys Glu Cys Thr Ser Leu Cys Cys Glu 435 440 445 GCCCTA ACG TGT AAA CTG AAG CCT GGA ACT GAT TGC GGA GGA GAT GCT 1452 Ala LeuThr Cys Lys Leu Lys Pro Gly Thr Asp Cys Gly Gly Asp Ala 450 455 460 CCAAAC CAT ACC ACA GAG TGAATCCAAA GTCTGCTTCA CTGAGATGCT 1500 Pro Asn HisThr Thr Glu 465 470 ACCTTGCCAG GACAAGAACC AAGAACTCTA ACTGTCCCAGGAATCTTGTG AATTTTCACC 1560 CATAATGGTC TTTCACTTGT CATTCTACTT TCTATATTGTTATCAGTCCA GGAAACAGGT 1620 AAACAGATGT AATTAGAGAC ATTGGCTCTT TGTTTAGGCCTAATCTTTCT TTTTACTTTT 1680 TTTTTTCTTT TTTCTTTTTT TTTAAAGATC ATGAATTTGTGACTTAGTTC TGCCCTTTGG 1740 AGAACAAAAG AAAGCAGTCT TCCATCAAAT CACCTTAAAATGCACGGCTA AACTATTCAG 1800 AGTTAACACT CCAGAATTGT TAAATTACAA GTACTATGCTTTAATGCTTC TTTCATCTTA 1860 CTAGTATGGC CTATAAAAAA AATAATACCA CTTGATGGGTGAAGGCTTTG GCAATAGAAA 1920 GAAGAATAGA ATTCAGGTTT TATGTTATTC CTCTGTGTTCACTTCGCCTT GCTCTTGAAA 1980 GTGCAGTATT TTTCTACATC ATGTCGAGAA TGATTCAATGTAAATATTTT TCATTTTATC 2040 ATGTATATCC TATACACACA TCTCCTTCAT CATCATATATGAAGTTTATT TTGAGAAGTC 2100 TACATTGCTT ACATTTTAAT TGAGCCAGCA AAGAAGGCTTAATGATTTAT TGAACCATAA 2160 TGTCAATAAA AACACAACTT TTGAGGCAAA AAAAAAAAAAAAAAAAAAAA AAAAAAAAAA 2220 AAAAAAAAAA AAAAAAAAAA AAGAAAAAAA AAAAAAAAAAAAAAAAGACC TGCCCGGGCG 2280 470 amino acids amino acid linear protein 2Met Leu Arg Gly Ile Ser Gln Leu Pro Ala Val Ala Thr Met Ser Trp 1 5 1015 Val Leu Leu Pro Val Leu Trp Leu Ile Val Gln Thr Gln Ala Ile Ala 20 2530 Ile Lys Gln Thr Pro Glu Leu Thr Leu His Glu Ile Val Cys Pro Lys 35 4045 Lys Leu His Ile Leu His Lys Arg Glu Ile Lys Asn Asn Gln Thr Glu 50 5560 Lys His Gly Lys Glu Glu Arg Tyr Glu Pro Glu Val Gln Tyr Gln Met 65 7075 80 Ile Leu Asn Gly Glu Glu Ile Ile Leu Ser Leu Gln Lys Thr Lys His 8590 95 Leu Leu Gly Pro Asp Tyr Thr Glu Thr Leu Tyr Ser Pro Arg Gly Glu100 105 110 Glu Ile Thr Thr Lys Pro Glu Asn Met Glu His Cys Tyr Tyr LysGly 115 120 125 Asn Ile Leu Asn Glu Lys Asn Ser Val Ala Ser Ile Ser ThrCys Asp 130 135 140 Gly Leu Arg Gly Tyr Phe Thr His His His Gln Arg TyrGln Ile Lys 145 150 155 160 Pro Leu Lys Ser Thr Asp Glu Lys Glu His AlaVal Phe Thr Ser Asn 165 170 175 Gln Glu Glu Gln Asp Pro Ala Asn His ThrCys Gly Val Lys Ser Thr 180 185 190 Asp Gly Lys Gln Gly Pro Ile Arg IleSer Arg Ser Leu Lys Ser Pro 195 200 205 Glu Lys Glu Asp Phe Leu Arg AlaGln Lys Tyr Ile Asp Leu Tyr Leu 210 215 220 Val Leu Asp Asn Ala Phe TyrLys Asn Tyr Asn Glu Asn Leu Thr Leu 225 230 235 240 Ile Arg Ser Phe ValPhe Asp Val Met Asn Leu Leu Asn Val Ile Tyr 245 250 255 Asn Thr Ile AspVal Gln Val Ala Leu Val Gly Met Glu Ile Trp Ser 260 265 270 Asp Gly AspLys Ile Lys Val Val Pro Ser Ala Ser Thr Thr Phe Asp 275 280 285 Asn PheLeu Arg Trp His Ser Ser Asn Pro Gly Lys Lys Ile His Asp 290 295 300 HisAla Gln Leu Leu Ser Gly Ile Ser Phe Asn Asn Arg Arg Val Gly 305 310 315320 Leu Ala Ala Ser Asn Ser Leu Cys Ser Pro Ser Ser Val Ala Val Ile 325330 335 Glu Ala Lys Lys Lys Asn Asn Val Ala Leu Val Gly Val Met Ser His340 345 350 Glu Leu Gly His Val Leu Gly Met Pro Asp Val Pro Phe Asn ThrLys 355 360 365 Cys Pro Ser Gly Ser Cys Val Met Asn Gln Tyr Leu Ser SerLys Phe 370 375 380 Pro Lys Asp Phe Ser Thr Ser Cys Arg Ala His Phe GluArg Tyr Leu 385 390 395 400 Leu Ser Gln Lys Pro Lys Cys Leu Leu Gln AlaPro Ile Pro Thr Asn 405 410 415 Ile Met Thr Thr Pro Val Cys Gly Asn HisLeu Leu Glu Val Gly Glu 420 425 430 Asp Cys Asp Cys Gly Ser Pro Lys GluCys Thr Ser Leu Cys Cys Glu 435 440 445 Ala Leu Thr Cys Lys Leu Lys ProGly Thr Asp Cys Gly Gly Asp Ala 450 455 460 Pro Asn His Thr Thr Glu 465470 1780 base pairs nucleic acid single linear cDNA CDS 66..1766 3AGTGGAGAGG ACCGCGCTGT CCTGCTGTCA CCAAGAGCTG GAGACACCAT CTCCCACCGA 60GAGTC ATG GCC CCA TTG GCC CTG CAC CTC CTC GTC CTC GTC CCC ATC 107 MetAla Pro Leu Ala Leu His Leu Leu Val Leu Val Pro Ile 1 5 10 CTC CTC AGCCTG GTG GCC TCC CAG GAC TGG AAG GCT GAA CGC AGC CAA 155 Leu Leu Ser LeuVal Ala Ser Gln Asp Trp Lys Ala Glu Arg Ser Gln 15 20 25 30 GAC CCC TTCGAG AAA TGC ATG CAG GAT CCT GAC TAT GAG CAG CTG CTC 203 Asp Pro Phe GluLys Cys Met Gln Asp Pro Asp Tyr Glu Gln Leu Leu 35 40 45 AAG GTG GTG ACCTGG GGG CTC AAT CGG ACC CTG AAG CCC CAG AGG GTG 251 Lys Val Val Thr TrpGly Leu Asn Arg Thr Leu Lys Pro Gln Arg Val 50 55 60 ATT GTG GTT GGC GCTGGT GTG GCC GGG CTG GTG GCC GCC AAG GTG CTC 299 Ile Val Val Gly Ala GlyVal Ala Gly Leu Val Ala Ala Lys Val Leu 65 70 75 AGC GAT GCT GGA CAC AAGGTC ACC ATC CTG GAG GCA GAT AAC AGG ATC 347 Ser Asp Ala Gly His Lys ValThr Ile Leu Glu Ala Asp Asn Arg Ile 80 85 90 GGG GGC CGC ATC TTC ACC TACCGG GAC CAG AAC ACG GGC TGG ATT GGG 395 Gly Gly Arg Ile Phe Thr Tyr ArgAsp Gln Asn Thr Gly Trp Ile Gly 95 100 105 110 GAG CTG GGA GCC ATG CGCATG CCC AGC TCT CAC AGG ATC CTC CAC AAG 443 Glu Leu Gly Ala Met Arg MetPro Ser Ser His Arg Ile Leu His Lys 115 120 125 CTC TGC CAG GGC CTG GGGCTC AAC CTG ACC AAG TTC ACC CAG TAC GAC 491 Leu Cys Gln Gly Leu Gly LeuAsn Leu Thr Lys Phe Thr Gln Tyr Asp 130 135 140 AAG AAC ACG TGG ACG GAGGTG CAC GAA GTG AAG CTG CGC AAC TAT GTG 539 Lys Asn Thr Trp Thr Glu ValHis Glu Val Lys Leu Arg Asn Tyr Val 145 150 155 GTG GAG AAG GTG CCC GAGAAG CTG GGC TAC GCC TTG CGT CCC CAG GAA 587 Val Glu Lys Val Pro Glu LysLeu Gly Tyr Ala Leu Arg Pro Gln Glu 160 165 170 AAG GGC CAC TCG CCC GAAGAC ATC TAC CAG ATG GCT CTC AAC CAG GCC 635 Lys Gly His Ser Pro Glu AspIle Tyr Gln Met Ala Leu Asn Gln Ala 175 180 185 190 CTC AAA GAC CTC AAGGCA CTG GGC TGC AGA AAG GCG ATG AAG AAG TTT 683 Leu Lys Asp Leu Lys AlaLeu Gly Cys Arg Lys Ala Met Lys Lys Phe 195 200 205 GAA AGG CAC ACG CTCTTG GAA TAT CTT CTC GGG GAG GGG AAC CTG AGC 731 Glu Arg His Thr Leu LeuGlu Tyr Leu Leu Gly Glu Gly Asn Leu Ser 210 215 220 CGG CCG GCC GTG CAGCTT CTG GGA GAC GTG ATG TCC GAG GAT GGC TTC 779 Arg Pro Ala Val Gln LeuLeu Gly Asp Val Met Ser Glu Asp Gly Phe 225 230 235 TTC TAT CTC AGC TTCGCC GAG GCC CTC CGG GCC CAC AGC TGC CTC AGC 827 Phe Tyr Leu Ser Phe AlaGlu Ala Leu Arg Ala His Ser Cys Leu Ser 240 245 250 GAC AGA CTC CAG TACAGC CGC ATC GTG GGT GGC TGG GAC CTG CTG CCG 875 Asp Arg Leu Gln Tyr SerArg Ile Val Gly Gly Trp Asp Leu Leu Pro 255 260 265 270 CGC GCG CTG CTGAGC TCG CTG TCC GGG CTT GTG CTG TTG AAC GCG CCC 923 Arg Ala Leu Leu SerSer Leu Ser Gly Leu Val Leu Leu Asn Ala Pro 275 280 285 GTG GTG GCG ATGACC CAG GGA CCG CAC GAT GTG CAC GTG CAG ATC GAG 971 Val Val Ala Met ThrGln Gly Pro His Asp Val His Val Gln Ile Glu 290 295 300 ACC TCT CCC CCGGCG CGG AAT CTG AAG GTG CTG AAG GCC GAC GTG GTG 1019 Thr Ser Pro Pro AlaArg Asn Leu Lys Val Leu Lys Ala Asp Val Val 305 310 315 CTG CTG ACG GCGAGC GGA CCG GCG GTG AAG CGC ATC ACC TTC TCG CCG 1067 Leu Leu Thr Ala SerGly Pro Ala Val Lys Arg Ile Thr Phe Ser Pro 320 325 330 CCG CTG CCC CGCCAC ATG CAG GAG GCG CTG CGG AGG CTG CAC TAC GTG 1115 Pro Leu Pro Arg HisMet Gln Glu Ala Leu Arg Arg Leu His Tyr Val 335 340 345 350 CCG GCC ACCAAG GTG TTC CTA AGC TTC CGC AGG CCC TTC TGG CGC GAG 1163 Pro Ala Thr LysVal Phe Leu Ser Phe Arg Arg Pro Phe Trp Arg Glu 355 360 365 GAG CAC ATTGAA GGC GGC CAC TCA AAC ACC GAT CGC CCG TCG CGC ATG 1211 Glu His Ile GluGly Gly His Ser Asn Thr Asp Arg Pro Ser Arg Met 370 375 380 ATT TTC TACCCG CCG CCG CGC GAG GGC GCG CTG CTG CTG GCC TCG TAC 1259 Ile Phe Tyr ProPro Pro Arg Glu Gly Ala Leu Leu Leu Ala Ser Tyr 385 390 395 ACG TGG TCGGAC GCG GCG GCA GCG TTC GCC GGC TTG AGC CGG GAA GAG 1307 Thr Trp Ser AspAla Ala Ala Ala Phe Ala Gly Leu Ser Arg Glu Glu 400 405 410 GCG TTG CGCTTG GCG CTC GAC GAC GTG GCG GCA TTG CAC GGG CCT GTC 1355 Ala Leu Arg LeuAla Leu Asp Asp Val Ala Ala Leu His Gly Pro Val 415 420 425 430 GTG CGCCAG CTC TGG GAC GGC ACC GGC GTC GTC AAG CGT TGG GCG GAG 1403 Val Arg GlnLeu Trp Asp Gly Thr Gly Val Val Lys Arg Trp Ala Glu 435 440 445 GAC CAGCAC AGC CAG GGT GGC TTT GTG GTA CAG CCG CCG GCG CTC TGG 1451 Asp Gln HisSer Gln Gly Gly Phe Val Val Gln Pro Pro Ala Leu Trp 450 455 460 CAA ACCGAA AAG GAT GAC TGG ACG GTC CCT TAT GGC CGC ATC TAC TTT 1499 Gln Thr GluLys Asp Asp Trp Thr Val Pro Tyr Gly Arg Ile Tyr Phe 465 470 475 GCC GGCGAG CAC ACC GCC TAC CCG CAC GGC TGG GTG GAG ACG GCG GTC 1547 Ala Gly GluHis Thr Ala Tyr Pro His Gly Trp Val Glu Thr Ala Val 480 485 490 AAG TCGGCG CTG CGC GCC GCC ATC AAG ATC AAC AGC CGG AAG GGG CCT 1595 Lys Ser AlaLeu Arg Ala Ala Ile Lys Ile Asn Ser Arg Lys Gly Pro 495 500 505 510 GCATCG GAC ACG GCC AGC CCC GAG GGG CAC GCA TCT GAC ATG GAG GGG 1643 Ala SerAsp Thr Ala Ser Pro Glu Gly His Ala Ser Asp Met Glu Gly 515 520 525 CAGGGG CAT GTG CAT GGG GTG GCC AGC AGC CCC TCG CAT GAC CTG GCA 1691 Gln GlyHis Val His Gly Val Ala Ser Ser Pro Ser His Asp Leu Ala 530 535 540 AAGGAA GAA GGC AGC CAC CCT CCA GTC CAA GGC CAG TTA TCT CTC CAA 1739 Lys GluGlu Gly Ser His Pro Pro Val Gln Gly Gln Leu Ser Leu Gln 545 550 555 AACACG ACC CAC ACG AGG ACC TCG CAT TAAAGTATTT TCGG 1780 Asn Thr Thr His ThrArg Thr Ser His 560 565 567 amino acids amino acid linear protein 4 MetAla Pro Leu Ala Leu His Leu Leu Val Leu Val Pro Ile Leu Leu 1 5 10 15Ser Leu Val Ala Ser Gln Asp Trp Lys Ala Glu Arg Ser Gln Asp Pro 20 25 30Phe Glu Lys Cys Met Gln Asp Pro Asp Tyr Glu Gln Leu Leu Lys Val 35 40 45Val Thr Trp Gly Leu Asn Arg Thr Leu Lys Pro Gln Arg Val Ile Val 50 55 60Val Gly Ala Gly Val Ala Gly Leu Val Ala Ala Lys Val Leu Ser Asp 65 70 7580 Ala Gly His Lys Val Thr Ile Leu Glu Ala Asp Asn Arg Ile Gly Gly 85 9095 Arg Ile Phe Thr Tyr Arg Asp Gln Asn Thr Gly Trp Ile Gly Glu Leu 100105 110 Gly Ala Met Arg Met Pro Ser Ser His Arg Ile Leu His Lys Leu Cys115 120 125 Gln Gly Leu Gly Leu Asn Leu Thr Lys Phe Thr Gln Tyr Asp LysAsn 130 135 140 Thr Trp Thr Glu Val His Glu Val Lys Leu Arg Asn Tyr ValVal Glu 145 150 155 160 Lys Val Pro Glu Lys Leu Gly Tyr Ala Leu Arg ProGln Glu Lys Gly 165 170 175 His Ser Pro Glu Asp Ile Tyr Gln Met Ala LeuAsn Gln Ala Leu Lys 180 185 190 Asp Leu Lys Ala Leu Gly Cys Arg Lys AlaMet Lys Lys Phe Glu Arg 195 200 205 His Thr Leu Leu Glu Tyr Leu Leu GlyGlu Gly Asn Leu Ser Arg Pro 210 215 220 Ala Val Gln Leu Leu Gly Asp ValMet Ser Glu Asp Gly Phe Phe Tyr 225 230 235 240 Leu Ser Phe Ala Glu AlaLeu Arg Ala His Ser Cys Leu Ser Asp Arg 245 250 255 Leu Gln Tyr Ser ArgIle Val Gly Gly Trp Asp Leu Leu Pro Arg Ala 260 265 270 Leu Leu Ser SerLeu Ser Gly Leu Val Leu Leu Asn Ala Pro Val Val 275 280 285 Ala Met ThrGln Gly Pro His Asp Val His Val Gln Ile Glu Thr Ser 290 295 300 Pro ProAla Arg Asn Leu Lys Val Leu Lys Ala Asp Val Val Leu Leu 305 310 315 320Thr Ala Ser Gly Pro Ala Val Lys Arg Ile Thr Phe Ser Pro Pro Leu 325 330335 Pro Arg His Met Gln Glu Ala Leu Arg Arg Leu His Tyr Val Pro Ala 340345 350 Thr Lys Val Phe Leu Ser Phe Arg Arg Pro Phe Trp Arg Glu Glu His355 360 365 Ile Glu Gly Gly His Ser Asn Thr Asp Arg Pro Ser Arg Met IlePhe 370 375 380 Tyr Pro Pro Pro Arg Glu Gly Ala Leu Leu Leu Ala Ser TyrThr Trp 385 390 395 400 Ser Asp Ala Ala Ala Ala Phe Ala Gly Leu Ser ArgGlu Glu Ala Leu 405 410 415 Arg Leu Ala Leu Asp Asp Val Ala Ala Leu HisGly Pro Val Val Arg 420 425 430 Gln Leu Trp Asp Gly Thr Gly Val Val LysArg Trp Ala Glu Asp Gln 435 440 445 His Ser Gln Gly Gly Phe Val Val GlnPro Pro Ala Leu Trp Gln Thr 450 455 460 Glu Lys Asp Asp Trp Thr Val ProTyr Gly Arg Ile Tyr Phe Ala Gly 465 470 475 480 Glu His Thr Ala Tyr ProHis Gly Trp Val Glu Thr Ala Val Lys Ser 485 490 495 Ala Leu Arg Ala AlaIle Lys Ile Asn Ser Arg Lys Gly Pro Ala Ser 500 505 510 Asp Thr Ala SerPro Glu Gly His Ala Ser Asp Met Glu Gly Gln Gly 515 520 525 His Val HisGly Val Ala Ser Ser Pro Ser His Asp Leu Ala Lys Glu 530 535 540 Glu GlySer His Pro Pro Val Gln Gly Gln Leu Ser Leu Gln Asn Thr 545 550 555 560Thr His Thr Arg Thr Ser His 565 2456 base pairs nucleic acid singlelinear cDNA CDS 69..1925 5 GGGTCGACCA CGCGTCCGAC CAGGTCGGGG CCGGGTTCCGGGTCGGGGAG CGGCTCCGGG 60 CGGCAGCT ATG AGG CGG GAC GTG CGC ATC CTG TTACTG GGC GAG GCC CAG 110 Met Arg Arg Asp Val Arg Ile Leu Leu Leu Gly GluAla Gln 1 5 10 GTG GGG AAG ACG TCG CTG ATC CTG TCC CTG GTG GGC GAG GAGTTC CCC 158 Val Gly Lys Thr Ser Leu Ile Leu Ser Leu Val Gly Glu Glu PhePro 15 20 25 30 GAG GAG GTC CCT CCC CGC GCG GAG GAG ATC ACG ATC CCC GCGGAC GTC 206 Glu Glu Val Pro Pro Arg Ala Glu Glu Ile Thr Ile Pro Ala AspVal 35 40 45 ACC CCG GAG AAG GTG CCC ACC CAC ATC GTG GAC TAC TCA GAA GCCGAG 254 Thr Pro Glu Lys Val Pro Thr His Ile Val Asp Tyr Ser Glu Ala Glu50 55 60 CAG ACG GAC GAG GAG CTG CGG GAG GAG ATC CAC AAG GCA AAC GTG GTG302 Gln Thr Asp Glu Glu Leu Arg Glu Glu Ile His Lys Ala Asn Val Val 6570 75 TGT GTG GTG TAT GAC GTC TCT GAG GAG GCC ACC ATT GAG AAG ATT CGA350 Cys Val Val Tyr Asp Val Ser Glu Glu Ala Thr Ile Glu Lys Ile Arg 8085 90 ACT AAG TGG ATC CCA CTG GTG AAT GGG GGG ACC ACG CAG GGG CCC AGG398 Thr Lys Trp Ile Pro Leu Val Asn Gly Gly Thr Thr Gln Gly Pro Arg 95100 105 110 GTG CCC ATC ATC CTA GTG GGC AAC AAG TCA GAC CTG CGG TCG GGGAGC 446 Val Pro Ile Ile Leu Val Gly Asn Lys Ser Asp Leu Arg Ser Gly Ser115 120 125 TCC ATG GAG GCC GTG CTC CCC ATC ATG AGC CAG TTT CCC GAG ATTGAG 494 Ser Met Glu Ala Val Leu Pro Ile Met Ser Gln Phe Pro Glu Ile Glu130 135 140 ACC TGC GTG GAG TGT TCG GCC AAG AAC CTG AGG AAC ATC TCA GAGCTG 542 Thr Cys Val Glu Cys Ser Ala Lys Asn Leu Arg Asn Ile Ser Glu Leu145 150 155 TTC TAC TAC GCC CAG AAG GCC GTC CTG CAT CCC ACA GCC CCC CTCTAT 590 Phe Tyr Tyr Ala Gln Lys Ala Val Leu His Pro Thr Ala Pro Leu Tyr160 165 170 GAC CCT GAG GCC AAG CAG TTG AGG CCC GCG TGC GCC CAG GCG CTGACG 638 Asp Pro Glu Ala Lys Gln Leu Arg Pro Ala Cys Ala Gln Ala Leu Thr175 180 185 190 CGC ATC TTC AGG CTC TCA GAT CAG GAC CTG GAC CAG GCG CTCAGT GAC 686 Arg Ile Phe Arg Leu Ser Asp Gln Asp Leu Asp Gln Ala Leu SerAsp 195 200 205 GAA GAG CTC AAC GCT TTC CAG CAG AAA TCC TGC TTT GGG CACCCC CTG 734 Glu Glu Leu Asn Ala Phe Gln Gln Lys Ser Cys Phe Gly His ProLeu 210 215 220 GCC CCG CAG GCC CTG GAG GAC GTG AAG ACG GTG GTG TGC AGGAAC GTG 782 Ala Pro Gln Ala Leu Glu Asp Val Lys Thr Val Val Cys Arg AsnVal 225 230 235 GCG GGC GGC GTG CGG GAG GAC CGG CTG ACC CTG GAT GGT TTCCTC TTC 830 Ala Gly Gly Val Arg Glu Asp Arg Leu Thr Leu Asp Gly Phe LeuPhe 240 245 250 CTG AAC ACG CTC TTC ATC CAG CGC GGC CGG CAC GAG ACC ACCTGG ACC 878 Leu Asn Thr Leu Phe Ile Gln Arg Gly Arg His Glu Thr Thr TrpThr 255 260 265 270 ATC CTG CGG CGC TTC GGC TAC AGC GAT GCC CTG GAG CTGACT GCG GAC 926 Ile Leu Arg Arg Phe Gly Tyr Ser Asp Ala Leu Glu Leu ThrAla Asp 275 280 285 TAT CTC TCC CCT CTG ATC CAC GTG CCC CCC GGC TGC AGCACG GAG CTC 974 Tyr Leu Ser Pro Leu Ile His Val Pro Pro Gly Cys Ser ThrGlu Leu 290 295 300 AAC CAC CTT GGC TAC CAG TTT GTG CAG AGA GTG TTT GAGAAG CAC GAC 1022 Asn His Leu Gly Tyr Gln Phe Val Gln Arg Val Phe Glu LysHis Asp 305 310 315 CAG GAC CGC GAC GGC GCC CTC TCG CCC GTG GAG CTG CAAAGC CTT TTC 1070 Gln Asp Arg Asp Gly Ala Leu Ser Pro Val Glu Leu Gln SerLeu Phe 320 325 330 AGT GTG TTC CCA GCA GCG CCC TGG GGC CCC GAG CTC CCACGC ACA GTC 1118 Ser Val Phe Pro Ala Ala Pro Trp Gly Pro Glu Leu Pro ArgThr Val 335 340 345 350 CGC ACA GAG GCC GGC CGG TTG CCC CTG CAC GGA TACCTC TGC CAG TGG 1166 Arg Thr Glu Ala Gly Arg Leu Pro Leu His Gly Tyr LeuCys Gln Trp 355 360 365 ACC CTG GTG ACC TAC CTG GAC GTC CGG AGC TGC CTTGGA CAC CTA GGC 1214 Thr Leu Val Thr Tyr Leu Asp Val Arg Ser Cys Leu GlyHis Leu Gly 370 375 380 TAC CTG GGC TAC CCC ACC CTC TGT GAG CAG GAC CAGGCC CAT GCC ATC 1262 Tyr Leu Gly Tyr Pro Thr Leu Cys Glu Gln Asp Gln AlaHis Ala Ile 385 390 395 ACA GTC ACT CGT GAG AAG AGG CTG GAC CAG GAG AAGGGA CAG ACG CAG 1310 Thr Val Thr Arg Glu Lys Arg Leu Asp Gln Glu Lys GlyGln Thr Gln 400 405 410 TGG AGC GTC CTC CTG TGC AAG GTG GTA GGG GCC CGTGGA GTG GGC AAG 1358 Trp Ser Val Leu Leu Cys Lys Val Val Gly Ala Arg GlyVal Gly Lys 415 420 425 430 TCT GCC TTC CTG CAG GCC TTT CTC GGC CGC GGCCTG GGG CAC CAG GAC 1406 Ser Ala Phe Leu Gln Ala Phe Leu Gly Arg Gly LeuGly His Gln Asp 435 440 445 ACG AGG GAG CAG CCT CCC GGC TAC GCC ATC GACACG GTG CAG GTC AAT 1454 Thr Arg Glu Gln Pro Pro Gly Tyr Ala Ile Asp ThrVal Gln Val Asn 450 455 460 GGA CAG GAG AAG TAC TTG ATC CTC TGT GAG GTGGGC ACA GAT GGT CTG 1502 Gly Gln Glu Lys Tyr Leu Ile Leu Cys Glu Val GlyThr Asp Gly Leu 465 470 475 CTG GCC ACA TCG CTG GAC GCC ACC TGT GAC GTTGCC TGC TTG ATG TTT 1550 Leu Ala Thr Ser Leu Asp Ala Thr Cys Asp Val AlaCys Leu Met Phe 480 485 490 GAT GGC AGT GAC CCA AAG TCC TTT GCA CAT TGTGCC AGC GTC TAC AAG 1598 Asp Gly Ser Asp Pro Lys Ser Phe Ala His Cys AlaSer Val Tyr Lys 495 500 505 510 CAC CAT TAC ATG GAC GGG CAG ACC CCC TGCCTC TTT GTC TCC TCC AAG 1646 His His Tyr Met Asp Gly Gln Thr Pro Cys LeuPhe Val Ser Ser Lys 515 520 525 GCC GAC CTG CCC GAA GGT GTC GCG GTG TCTGGC CCA TCA CCG GCC GAG 1694 Ala Asp Leu Pro Glu Gly Val Ala Val Ser GlyPro Ser Pro Ala Glu 530 535 540 TTT TGC CGC AAG CAC CGG CTA CCC GCT CCCGTG CCG TTC TCC TGT GCT 1742 Phe Cys Arg Lys His Arg Leu Pro Ala Pro ValPro Phe Ser Cys Ala 545 550 555 GGC CCA GCC GAG CCC AGC ACC ACC ATC TTCACC CAG CTC GCC ACC ATG 1790 Gly Pro Ala Glu Pro Ser Thr Thr Ile Phe ThrGln Leu Ala Thr Met 560 565 570 GCC GCC TTC CCA CAT TTG GTC CAC GCA GAGCTG CAT CCC TCT TCC TTC 1838 Ala Ala Phe Pro His Leu Val His Ala Glu LeuHis Pro Ser Ser Phe 575 580 585 590 TGG CTC CGG GGG CTG CTG GGG GTT GTCGGG GCC GCC GTG GCC GCA GTC 1886 Trp Leu Arg Gly Leu Leu Gly Val Val GlyAla Ala Val Ala Ala Val 595 600 605 CTC AGC TTC TCA CTC TAC AGG GTC CTGGTG AAG AGC CAG TGAGGCCCCT 1935 Leu Ser Phe Ser Leu Tyr Arg Val Leu ValLys Ser Gln 610 615 GGTACCCAAG CCCCCTCCCC TGACCTGGGT GTGCCTCGCTGCTGGGGCTC TGCACTTTTT 1995 GTTTCTGAAG GCAGTCGATC TGCAGCGGGG CCTTATGCTGCCATGCACTG CCCTGGCTCC 2055 TGCCGGACCC CCAGGGTGGG CCGTGGCAGG TGGCTGAGCAGGAGCTCCCA AGTGCCGGCC 2115 ACCGCTGTCA GGGATTGCCC ACCCCTGGGC ATCATGTGTGTGGGGCCGGG GAGCACAGGT 2175 GTGGGAGCTG GTGACCCCAG ACCCAGAATT CTCAGGGCTCTACCCCCCTT TCCTGGTCCT 2235 AGGTGGCCAG TGGGTATGAG GAGGGCTGGA AGGCAGAGCTTTGGGCCAAA AGCAGGCGTT 2295 GGGGGGTCCC CCCTCAAGTT TGGAGCCGTT TCCGTGGTTGTAGCAGAGGA CCGGAGGTTG 2355 GGTTCCTGAT TAAACTTCAC TGTGTGTTTT CTATCTCGGATCCCAGTCTC TGAAGACAAC 2415 TTGCTTTGAT TCAACCTAAA AAAAAAAAAA AAAAAAAAAA A2456 619 amino acids amino acid linear protein 6 Met Arg Arg Asp Val ArgIle Leu Leu Leu Gly Glu Ala Gln Val Gly 1 5 10 15 Lys Thr Ser Leu IleLeu Ser Leu Val Gly Glu Glu Phe Pro Glu Glu 20 25 30 Val Pro Pro Arg AlaGlu Glu Ile Thr Ile Pro Ala Asp Val Thr Pro 35 40 45 Glu Lys Val Pro ThrHis Ile Val Asp Tyr Ser Glu Ala Glu Gln Thr 50 55 60 Asp Glu Glu Leu ArgGlu Glu Ile His Lys Ala Asn Val Val Cys Val 65 70 75 80 Val Tyr Asp ValSer Glu Glu Ala Thr Ile Glu Lys Ile Arg Thr Lys 85 90 95 Trp Ile Pro LeuVal Asn Gly Gly Thr Thr Gln Gly Pro Arg Val Pro 100 105 110 Ile Ile LeuVal Gly Asn Lys Ser Asp Leu Arg Ser Gly Ser Ser Met 115 120 125 Glu AlaVal Leu Pro Ile Met Ser Gln Phe Pro Glu Ile Glu Thr Cys 130 135 140 ValGlu Cys Ser Ala Lys Asn Leu Arg Asn Ile Ser Glu Leu Phe Tyr 145 150 155160 Tyr Ala Gln Lys Ala Val Leu His Pro Thr Ala Pro Leu Tyr Asp Pro 165170 175 Glu Ala Lys Gln Leu Arg Pro Ala Cys Ala Gln Ala Leu Thr Arg Ile180 185 190 Phe Arg Leu Ser Asp Gln Asp Leu Asp Gln Ala Leu Ser Asp GluGlu 195 200 205 Leu Asn Ala Phe Gln Gln Lys Ser Cys Phe Gly His Pro LeuAla Pro 210 215 220 Gln Ala Leu Glu Asp Val Lys Thr Val Val Cys Arg AsnVal Ala Gly 225 230 235 240 Gly Val Arg Glu Asp Arg Leu Thr Leu Asp GlyPhe Leu Phe Leu Asn 245 250 255 Thr Leu Phe Ile Gln Arg Gly Arg His GluThr Thr Trp Thr Ile Leu 260 265 270 Arg Arg Phe Gly Tyr Ser Asp Ala LeuGlu Leu Thr Ala Asp Tyr Leu 275 280 285 Ser Pro Leu Ile His Val Pro ProGly Cys Ser Thr Glu Leu Asn His 290 295 300 Leu Gly Tyr Gln Phe Val GlnArg Val Phe Glu Lys His Asp Gln Asp 305 310 315 320 Arg Asp Gly Ala LeuSer Pro Val Glu Leu Gln Ser Leu Phe Ser Val 325 330 335 Phe Pro Ala AlaPro Trp Gly Pro Glu Leu Pro Arg Thr Val Arg Thr 340 345 350 Glu Ala GlyArg Leu Pro Leu His Gly Tyr Leu Cys Gln Trp Thr Leu 355 360 365 Val ThrTyr Leu Asp Val Arg Ser Cys Leu Gly His Leu Gly Tyr Leu 370 375 380 GlyTyr Pro Thr Leu Cys Glu Gln Asp Gln Ala His Ala Ile Thr Val 385 390 395400 Thr Arg Glu Lys Arg Leu Asp Gln Glu Lys Gly Gln Thr Gln Trp Ser 405410 415 Val Leu Leu Cys Lys Val Val Gly Ala Arg Gly Val Gly Lys Ser Ala420 425 430 Phe Leu Gln Ala Phe Leu Gly Arg Gly Leu Gly His Gln Asp ThrArg 435 440 445 Glu Gln Pro Pro Gly Tyr Ala Ile Asp Thr Val Gln Val AsnGly Gln 450 455 460 Glu Lys Tyr Leu Ile Leu Cys Glu Val Gly Thr Asp GlyLeu Leu Ala 465 470 475 480 Thr Ser Leu Asp Ala Thr Cys Asp Val Ala CysLeu Met Phe Asp Gly 485 490 495 Ser Asp Pro Lys Ser Phe Ala His Cys AlaSer Val Tyr Lys His His 500 505 510 Tyr Met Asp Gly Gln Thr Pro Cys LeuPhe Val Ser Ser Lys Ala Asp 515 520 525 Leu Pro Glu Gly Val Ala Val SerGly Pro Ser Pro Ala Glu Phe Cys 530 535 540 Arg Lys His Arg Leu Pro AlaPro Val Pro Phe Ser Cys Ala Gly Pro 545 550 555 560 Ala Glu Pro Ser ThrThr Ile Phe Thr Gln Leu Ala Thr Met Ala Ala 565 570 575 Phe Pro His LeuVal His Ala Glu Leu His Pro Ser Ser Phe Trp Leu 580 585 590 Arg Gly LeuLeu Gly Val Val Gly Ala Ala Val Ala Ala Val Leu Ser 595 600 605 Phe SerLeu Tyr Arg Val Leu Val Lys Ser Gln 610 615

What is claimed is:
 1. A compound selected from the group consisting of:a) a binding compound comprising an antibody binding site whichspecifically binds to: i) primate BS10.55 protein; or ii) primate YTF03protein. b) a nucleic acid comprising sequence encoding at least 12amino acids of: i) primate BS10.55 protein; or ii) primate YTF03protein; c) a substantially pure protein which is specificallyrecognized by said antibody binding site of (a); d) a substantially pureprimate BS10.55, or primate YTF03 protein or peptide thereof, and; e) afusion protein comprising a 30 amino acid sequence portion of primateBS10.55, or primate YTF03 protein sequence.
 2. The composition of claim1a, wherein said antibody binding site: a) is specificallyimmunoreactive with a protein selected from polypeptides of SEQ ID NO: 2and 4; b) is raised against a purified or recombinantly produced primateBS10.55, or primate YTF03 protein; c) is immunoselected on asubstantially purified or recombinantly produced primate BS10.55, orprimate YTF03 protein; d) is in a monoclonal antibody, Fab, or F(ab)₂;e) is detectably labeled; f) is attached to a solid substrate; g) isfrom a rabbit or mouse; h) binds with a Kd of at least about 300 μM; i)is fused to another protein segment; j) is in a chimeric antibody; or k)is couped to another chemical moiety.
 3. A method of making anantigen-antibody complex, comprising a step of contacting a primatebiological sample to a specific binding antibody of claim
 2. 4. Themethod of claim 3, which further purifies said antigen or said antibody.5. The antibody binding site of claim 1a, wherein said binding site isdetected in a biological sample by a method comprising the steps of: a)contacting a binding agent having an affinity for said BS10.55, or YTF03protein with said biological sample; b) incubating said binding agentwith said biological sample to form a binding agent:BS10.55, or YTF03protein complex; and c) detecting said complex.
 6. The method of claim5, wherein said biological sample is human, and wherein said bindingagent is an antibody.
 7. A kit comprising a composition of claim 1,wherein said kit further comprises: a) instructional material for theuse of said composition; or b) segregation of said composition into acontainer.
 8. The kit of claim 7, wherein said kit is used to make aqualitative or quantitative analysis.
 9. A cell selected from the groupconsisting of: a) a cell comprising an antibody of claim 1a; b) a celltransfected with a nucleic acid of claim 1b; c) a cell comprising afusion protein of claim 1e.
 10. The nucleic acid of claim 1b, encoding apolypeptide, wherein said polypeptide specifically binds an antibodygenerated against an immunogen selected from the group consisting of themature polypeptides of SEQ ID NO: 2 and
 4. 11. The nucleic acid of claim1b which: a) encodes at least 12 amino acids of: i) SEQ ID NO: 2; or ii)SEQ ID NO: 4; b) comprises sequence of at least about 39 nucleotidesselected from the group consisting of the protein coding portions of SEQID NO: 1 and 3; c) hybridizes to SEQ ID NO: 1 or 3 under stringent washconditions of at least 45° C. and less than about 150 mM salt; d)comprises sequence made by a synthetic method; e) is an expressionvector; f) is detectably labeled; g) is attached to a solid substrate;h) is from human; i) binds with a Kd of at least about 300 μM; j) isfused to another nucleic acid segment; k) is coupled to another chemicalmoiety; l) is operably associated with promoter, ribosome binding site,or poly-A addition site; m) is a PCR product; n) is transformed into acell, including a bacterial cell; o) is in a sterile composition; p) iscapable of selectively hybridizing to a nucleic acid encoding a BS10.55,or YTF03 protein; q) which comprises a natural sequence; r) comprises amature protein coding segment of SEQ ID NO: 1 or 3; s) which encodesproteolytically active portion of BS10.55; or t) which encodes anoxidoreductive active portion of YTF03.
 12. The nucleic acid of claim1b, wherein said isolated nucleic acid is detected in a biologicalsample by a method comprising: a) contacting said biological sample witha nucleic acid probe capable of selectively hybridizing to said nucleicacid; b) incubating said nucleic acid probe with the biological sampleto form a hybrid of the nucleic acid probe with complementary nucleicacid sequences present in the biological sample; and c) determining theextent of hybridization of the nucleic acid probe to the complementarynucleic acid sequences.
 13. The method of claim 12, wherein said nucleicacid probe is capable of hybridizing to a nucleic acid encoding aprotein selected from the group consisting of the mature polypeptides ofSEQ ID NO 2 and
 4. 14. The protein of claim 1c or 1d, which: a) bindswith a Kd of at least about 300 μM to an antibody generated against animmunogen of the polypeptides of SEQ ID NO: 2 or 4; b) is immunoselectedon an antibody which selectively binds a polypeptide of SEQ ID NO: 2 or4; c) comprises sequence of at least 12 contiguous residues of SEQ IDNO: 2 or 4; d) exhibits a post-translational modification patterndistinct from natural BS10.55, or YTF03; e) is 3-fold or fewersubstituted from natural sequence; f) is recombinantly produced; g) isdenatured; h) has sequence of full length natural polypeptide; i) isdetectably labeled; j) is attached to a solid substrate; k) is fromhuman; l) is in a sterile composition; m) is fused to another proteinsegment; n) is coupled to another chemical moiety; o) comprises at leasta fragment of at least 32 amino acid residues from a human BS10.55, orhuman YTF03 protein; p) comprises mature polypeptide sequence selectedfrom the group consisting of SEQ ID NO 2 and 4; q) is a soluble protein;r) is a naturally occurring protein; s) which is a proteolyticallyactive portion of BS10.55; or t) which is an oxidoreductive activeportion of YTF03.
 15. An isolated protein, which specifically binds toan antibody generated against an immunogen selected from the groupconsisting of the full length polypeptides of: a) SEQ ID NO: 2; and b)SEQ ID NO:
 4. 16. The protein of claim 15, which: a) binds to saidantibody with a Kd of at least about 300 μM; b) is immunoselected on anantibody which selectively binds a polypeptide of SEQ ID NO: 2 or 4; c)comprises sequence of at least 12 contiguous residues of SEQ ID NO: 2 or4; d) exhibits a post-translational modification pattern distinct fromnatural BS10.55, or YTF03; e) is 3-fold or fewer substituted fromnatural sequence; f) is recombinantly produced; g) is denatured; h) hassequence of full length natural polypeptide; i) is detectably labeled;j) is attached to a solid substrate; k) is from human; l) is in asterile composition m) is fused to another protein segment; n) iscoupled to another chemical moiety o) comprises at least a fragment ofat least 32 amino acid residues from a human BS10.55, or human YTF03protein; p) comprises mature polypeptide sequence selected from thegroup consisting of SEQ ID NO 2 and 4; q) is a soluble protein; r) whichcomprises a proteolytic activity of BS10.55; or s) which comprises anoxidoreductive activity of YTF03.
 17. The fusion protein of claim 1e,which comprises sequence from an enzymatically active portion of SEQ IDNO: 2 or
 4. 18. The protein of claim 17, which: a) binds with a Kd of atleast about 300 μM to an antibody generated against an immunogenselected from the group consisting of the polypeptides of: i) SEQ ID NO.2; and ii) SEQ ID NO. 4; b) is immunoselected on an antibody whichselectively binds a polypeptide of SEQ ID NO: 2 or 4; c) comprisessequence of at least 12 contiguous residues of SEQ ID NO: 2 or 4; d) isrecombinantly produced; e) is denatured; f) has sequence of full lengthnatural polypeptide; g) is detectably labeled; h) is attached to a solidsubstrate; i) comprises sequence from human; j) is in a sterilecomposition k) is fused to another protein segment; l) is coupled toanother chemical moiety m) comprises at least a fragment of at least 32amino acid residues from a human BS10.55, or human YTF03 protein; n)comprises mature polypeptide sequence selected from the group consistingof SEQ ID NO 2 and 4; o) is a soluble protein; p) which comprises aproteolytic activity of BS10.55; or q) which comprises an oxidoreductiveactivity of YTF03.
 19. A method of modulating physiology or developmentof a cell comprising contacting said cell with a composition of claim 1.20. A compound selected from the group consisting of: a) a bindingcompound comprising an antibody binding site which specifically binds toprimate APD08; b) a nucleic acid comprising sequence encoding at least12 amino acids of primate APD08; c) a substantially pure protein whichis specifically recognized by said antibody binding site of (a); d) asubstantially pure primate APD08 protein or peptide thereof, and; e) afusion protein comprising a 30 amino acid sequence portion of primateAPD08 protein sequence.